@datagrok/helm 3.0.1 → 3.0.3

package/dist/489.js.map

@@ -0,0 +1 @@
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* @module LRUCache\n */\nconst perf = typeof performance === 'object' &&\n    performance &&\n    typeof performance.now === 'function'\n    ? performance\n    : Date;\nconst warned = new Set();\n/* c8 ignore start */\nconst PROCESS = (typeof process === 'object' && !!process ? process : {});\n/* c8 ignore start */\nconst emitWarning = (msg, type, code, fn) => {\n    typeof PROCESS.emitWarning === 'function'\n        ? PROCESS.emitWarning(msg, type, code, fn)\n        : console.error(`[${code}] ${type}: ${msg}`);\n};\nlet AC = globalThis.AbortController;\nlet AS = globalThis.AbortSignal;\n/* c8 ignore start */\nif (typeof AC === 'undefined') {\n    //@ts-ignore\n    AS = class AbortSignal {\n        onabort;\n        _onabort = [];\n        reason;\n        aborted = false;\n        addEventListener(_, fn) {\n            this._onabort.push(fn);\n        }\n    };\n    //@ts-ignore\n    AC = class AbortController {\n        constructor() {\n            warnACPolyfill();\n        }\n        signal = new AS();\n        abort(reason) {\n            if (this.signal.aborted)\n                return;\n            //@ts-ignore\n            this.signal.reason = reason;\n            //@ts-ignore\n            this.signal.aborted = true;\n            //@ts-ignore\n            for (const fn of this.signal._onabort) {\n                fn(reason);\n            }\n            this.signal.onabort?.(reason);\n        }\n    };\n    let printACPolyfillWarning = PROCESS.env?.LRU_CACHE_IGNORE_AC_WARNING !== '1';\n    const warnACPolyfill = () => {\n        if (!printACPolyfillWarning)\n            return;\n        printACPolyfillWarning = false;\n        emitWarning('AbortController is not defined. If using lru-cache in ' +\n            'node 14, load an AbortController polyfill from the ' +\n            '`node-abort-controller` package. A minimal polyfill is ' +\n            'provided for use by LRUCache.fetch(), but it should not be ' +\n            'relied upon in other contexts (eg, passing it to other APIs that ' +\n            'use AbortController/AbortSignal might have undesirable effects). ' +\n            'You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.', 'NO_ABORT_CONTROLLER', 'ENOTSUP', warnACPolyfill);\n    };\n}\n/* c8 ignore stop */\nconst shouldWarn = (code) => !warned.has(code);\nconst TYPE = Symbol('type');\nconst isPosInt = (n) => n && n === Math.floor(n) && n > 0 && isFinite(n);\n/* c8 ignore start */\n// This is a little bit ridiculous, tbh.\n// The maximum array length is 2^32-1 or thereabouts on most JS impls.\n// And well before that point, you're caching the entire world, I mean,\n// that's ~32GB of just integers for the next/prev links, plus whatever\n// else to hold that many keys and values.  Just filling the memory with\n// zeroes at init time is brutal when you get that big.\n// But why not be complete?\n// Maybe in the future, these limits will have expanded.\nconst getUintArray = (max) => !isPosInt(max)\n    ? null\n    : max <= Math.pow(2, 8)\n        ? Uint8Array\n        : max <= Math.pow(2, 16)\n            ? Uint16Array\n            : max <= Math.pow(2, 32)\n                ? Uint32Array\n                : max <= Number.MAX_SAFE_INTEGER\n                    ? ZeroArray\n                    : null;\n/* c8 ignore stop */\nclass ZeroArray extends Array {\n    constructor(size) {\n        super(size);\n        this.fill(0);\n    }\n}\nclass Stack {\n    heap;\n    length;\n    // private constructor\n    static #constructing = false;\n    static create(max) {\n        const HeapCls = getUintArray(max);\n        if (!HeapCls)\n            return [];\n        Stack.#constructing = true;\n        const s = new Stack(max, HeapCls);\n        Stack.#constructing = false;\n        return s;\n    }\n    constructor(max, HeapCls) {\n        /* c8 ignore start */\n        if (!Stack.#constructing) {\n            throw new TypeError('instantiate Stack using Stack.create(n)');\n        }\n        /* c8 ignore stop */\n        this.heap = new HeapCls(max);\n        this.length = 0;\n    }\n    push(n) {\n        this.heap[this.length++] = n;\n    }\n    pop() {\n        return this.heap[--this.length];\n    }\n}\n/**\n * Default export, the thing you're using this module to get.\n *\n * The `K` and `V` types define the key and value types, respectively. The\n * optional `FC` type defines the type of the `context` object passed to\n * `cache.fetch()` and `cache.memo()`.\n *\n * Keys and values **must not** be `null` or `undefined`.\n *\n * All properties from the options object (with the exception of `max`,\n * `maxSize`, `fetchMethod`, `memoMethod`, `dispose` and `disposeAfter`) are\n * added as normal public members. (The listed options are read-only getters.)\n *\n * Changing any of these will alter the defaults for subsequent method calls.\n */\nexport class LRUCache {\n    // options that cannot be changed without disaster\n    #max;\n    #maxSize;\n    #dispose;\n    #disposeAfter;\n    #fetchMethod;\n    #memoMethod;\n    /**\n     * {@link LRUCache.OptionsBase.ttl}\n     */\n    ttl;\n    /**\n     * {@link LRUCache.OptionsBase.ttlResolution}\n     */\n    ttlResolution;\n    /**\n     * {@link LRUCache.OptionsBase.ttlAutopurge}\n     */\n    ttlAutopurge;\n    /**\n     * {@link LRUCache.OptionsBase.updateAgeOnGet}\n     */\n    updateAgeOnGet;\n    /**\n     * {@link LRUCache.OptionsBase.updateAgeOnHas}\n     */\n    updateAgeOnHas;\n    /**\n     * {@link LRUCache.OptionsBase.allowStale}\n     */\n    allowStale;\n    /**\n     * {@link LRUCache.OptionsBase.noDisposeOnSet}\n     */\n    noDisposeOnSet;\n    /**\n     * {@link LRUCache.OptionsBase.noUpdateTTL}\n     */\n    noUpdateTTL;\n    /**\n     * {@link LRUCache.OptionsBase.maxEntrySize}\n     */\n    maxEntrySize;\n    /**\n     * {@link LRUCache.OptionsBase.sizeCalculation}\n     */\n    sizeCalculation;\n    /**\n     * {@link LRUCache.OptionsBase.noDeleteOnFetchRejection}\n     */\n    noDeleteOnFetchRejection;\n    /**\n     * {@link LRUCache.OptionsBase.noDeleteOnStaleGet}\n     */\n    noDeleteOnStaleGet;\n    /**\n     * {@link LRUCache.OptionsBase.allowStaleOnFetchAbort}\n     */\n    allowStaleOnFetchAbort;\n    /**\n     * {@link LRUCache.OptionsBase.allowStaleOnFetchRejection}\n     */\n    allowStaleOnFetchRejection;\n    /**\n     * {@link LRUCache.OptionsBase.ignoreFetchAbort}\n     */\n    ignoreFetchAbort;\n    // computed properties\n    #size;\n    #calculatedSize;\n    #keyMap;\n    #keyList;\n    #valList;\n    #next;\n    #prev;\n    #head;\n    #tail;\n    #free;\n    #disposed;\n    #sizes;\n    #starts;\n    #ttls;\n    #hasDispose;\n    #hasFetchMethod;\n    #hasDisposeAfter;\n    /**\n     * Do not call this method unless you need to inspect the\n     * inner workings of the cache.  If anything returned by this\n     * object is modified in any way, strange breakage may occur.\n     *\n     * These fields are private for a reason!\n     *\n     * @internal\n     */\n    static unsafeExposeInternals(c) {\n        return {\n            // properties\n            starts: c.#starts,\n            ttls: c.#ttls,\n            sizes: c.#sizes,\n            keyMap: c.#keyMap,\n            keyList: c.#keyList,\n            valList: c.#valList,\n            next: c.#next,\n            prev: c.#prev,\n            get head() {\n                return c.#head;\n            },\n            get tail() {\n                return c.#tail;\n            },\n            free: c.#free,\n            // methods\n            isBackgroundFetch: (p) => c.#isBackgroundFetch(p),\n            backgroundFetch: (k, index, options, context) => c.#backgroundFetch(k, index, options, context),\n            moveToTail: (index) => c.#moveToTail(index),\n            indexes: (options) => c.#indexes(options),\n            rindexes: (options) => c.#rindexes(options),\n            isStale: (index) => c.#isStale(index),\n        };\n    }\n    // Protected read-only members\n    /**\n     * {@link LRUCache.OptionsBase.max} (read-only)\n     */\n    get max() {\n        return this.#max;\n    }\n    /**\n     * {@link LRUCache.OptionsBase.maxSize} (read-only)\n     */\n    get maxSize() {\n        return this.#maxSize;\n    }\n    /**\n     * The total computed size of items in the cache (read-only)\n     */\n    get calculatedSize() {\n        return this.#calculatedSize;\n    }\n    /**\n     * The number of items stored in the cache (read-only)\n     */\n    get size() {\n        return this.#size;\n    }\n    /**\n     * {@link LRUCache.OptionsBase.fetchMethod} (read-only)\n     */\n    get fetchMethod() {\n        return this.#fetchMethod;\n    }\n    get memoMethod() {\n        return this.#memoMethod;\n    }\n    /**\n     * {@link LRUCache.OptionsBase.dispose} (read-only)\n     */\n    get dispose() {\n        return this.#dispose;\n    }\n    /**\n     * {@link LRUCache.OptionsBase.disposeAfter} (read-only)\n     */\n    get disposeAfter() {\n        return this.#disposeAfter;\n    }\n    constructor(options) {\n        const { max = 0, ttl, ttlResolution = 1, ttlAutopurge, updateAgeOnGet, updateAgeOnHas, allowStale, dispose, disposeAfter, noDisposeOnSet, noUpdateTTL, maxSize = 0, maxEntrySize = 0, sizeCalculation, fetchMethod, memoMethod, noDeleteOnFetchRejection, noDeleteOnStaleGet, allowStaleOnFetchRejection, allowStaleOnFetchAbort, ignoreFetchAbort, } = options;\n        if (max !== 0 && !isPosInt(max)) {\n            throw new TypeError('max option must be a nonnegative integer');\n        }\n        const UintArray = max ? getUintArray(max) : Array;\n        if (!UintArray) {\n            throw new Error('invalid max value: ' + max);\n        }\n        this.#max = max;\n        this.#maxSize = maxSize;\n        this.maxEntrySize = maxEntrySize || this.#maxSize;\n        this.sizeCalculation = sizeCalculation;\n        if (this.sizeCalculation) {\n            if (!this.#maxSize && !this.maxEntrySize) {\n                throw new TypeError('cannot set sizeCalculation without setting maxSize or maxEntrySize');\n            }\n            if (typeof this.sizeCalculation !== 'function') {\n                throw new TypeError('sizeCalculation set to non-function');\n            }\n        }\n        if (memoMethod !== undefined &&\n            typeof memoMethod !== 'function') {\n            throw new TypeError('memoMethod must be a function if defined');\n        }\n        this.#memoMethod = memoMethod;\n        if (fetchMethod !== undefined &&\n            typeof fetchMethod !== 'function') {\n            throw new TypeError('fetchMethod must be a function if specified');\n        }\n        this.#fetchMethod = fetchMethod;\n        this.#hasFetchMethod = !!fetchMethod;\n        this.#keyMap = new Map();\n        this.#keyList = new Array(max).fill(undefined);\n        this.#valList = new Array(max).fill(undefined);\n        this.#next = new UintArray(max);\n        this.#prev = new UintArray(max);\n        this.#head = 0;\n        this.#tail = 0;\n        this.#free = Stack.create(max);\n        this.#size = 0;\n        this.#calculatedSize = 0;\n        if (typeof dispose === 'function') {\n            this.#dispose = dispose;\n        }\n        if (typeof disposeAfter === 'function') {\n            this.#disposeAfter = disposeAfter;\n            this.#disposed = [];\n        }\n        else {\n            this.#disposeAfter = undefined;\n            this.#disposed = undefined;\n        }\n        this.#hasDispose = !!this.#dispose;\n        this.#hasDisposeAfter = !!this.#disposeAfter;\n        this.noDisposeOnSet = !!noDisposeOnSet;\n        this.noUpdateTTL = !!noUpdateTTL;\n        this.noDeleteOnFetchRejection = !!noDeleteOnFetchRejection;\n        this.allowStaleOnFetchRejection = !!allowStaleOnFetchRejection;\n        this.allowStaleOnFetchAbort = !!allowStaleOnFetchAbort;\n        this.ignoreFetchAbort = !!ignoreFetchAbort;\n        // NB: maxEntrySize is set to maxSize if it's set\n        if (this.maxEntrySize !== 0) {\n            if (this.#maxSize !== 0) {\n                if (!isPosInt(this.#maxSize)) {\n                    throw new TypeError('maxSize must be a positive integer if specified');\n                }\n            }\n            if (!isPosInt(this.maxEntrySize)) {\n                throw new TypeError('maxEntrySize must be a positive integer if specified');\n            }\n            this.#initializeSizeTracking();\n        }\n        this.allowStale = !!allowStale;\n        this.noDeleteOnStaleGet = !!noDeleteOnStaleGet;\n        this.updateAgeOnGet = !!updateAgeOnGet;\n        this.updateAgeOnHas = !!updateAgeOnHas;\n        this.ttlResolution =\n            isPosInt(ttlResolution) || ttlResolution === 0\n                ? ttlResolution\n                : 1;\n        this.ttlAutopurge = !!ttlAutopurge;\n        this.ttl = ttl || 0;\n        if (this.ttl) {\n            if (!isPosInt(this.ttl)) {\n                throw new TypeError('ttl must be a positive integer if specified');\n            }\n            this.#initializeTTLTracking();\n        }\n        // do not allow completely unbounded caches\n        if (this.#max === 0 && this.ttl === 0 && this.#maxSize === 0) {\n            throw new TypeError('At least one of max, maxSize, or ttl is required');\n        }\n        if (!this.ttlAutopurge && !this.#max && !this.#maxSize) {\n            const code = 'LRU_CACHE_UNBOUNDED';\n            if (shouldWarn(code)) {\n                warned.add(code);\n                const msg = 'TTL caching without ttlAutopurge, max, or maxSize can ' +\n                    'result in unbounded memory consumption.';\n                emitWarning(msg, 'UnboundedCacheWarning', code, LRUCache);\n            }\n        }\n    }\n    /**\n     * Return the number of ms left in the item's TTL. If item is not in cache,\n     * returns `0`. Returns `Infinity` if item is in cache without a defined TTL.\n     */\n    getRemainingTTL(key) {\n        return this.#keyMap.has(key) ? Infinity : 0;\n    }\n    #initializeTTLTracking() {\n        const ttls = new ZeroArray(this.#max);\n        const starts = new ZeroArray(this.#max);\n        this.#ttls = ttls;\n        this.#starts = starts;\n        this.#setItemTTL = (index, ttl, start = perf.now()) => {\n            starts[index] = ttl !== 0 ? start : 0;\n            ttls[index] = ttl;\n            if (ttl !== 0 && this.ttlAutopurge) {\n                const t = setTimeout(() => {\n                    if (this.#isStale(index)) {\n                        this.#delete(this.#keyList[index], 'expire');\n                    }\n                }, ttl + 1);\n                // unref() not supported on all platforms\n                /* c8 ignore start */\n                if (t.unref) {\n                    t.unref();\n                }\n                /* c8 ignore stop */\n            }\n        };\n        this.#updateItemAge = index => {\n            starts[index] = ttls[index] !== 0 ? perf.now() : 0;\n        };\n        this.#statusTTL = (status, index) => {\n            if (ttls[index]) {\n                const ttl = ttls[index];\n                const start = starts[index];\n                /* c8 ignore next */\n                if (!ttl || !start)\n                    return;\n                status.ttl = ttl;\n                status.start = start;\n                status.now = cachedNow || getNow();\n                const age = status.now - start;\n                status.remainingTTL = ttl - age;\n            }\n        };\n        // debounce calls to perf.now() to 1s so we're not hitting\n        // that costly call repeatedly.\n        let cachedNow = 0;\n        const getNow = () => {\n            const n = perf.now();\n            if (this.ttlResolution > 0) {\n                cachedNow = n;\n                const t = setTimeout(() => (cachedNow = 0), this.ttlResolution);\n                // not available on all platforms\n                /* c8 ignore start */\n                if (t.unref) {\n                    t.unref();\n                }\n                /* c8 ignore stop */\n            }\n            return n;\n        };\n        this.getRemainingTTL = key => {\n            const index = this.#keyMap.get(key);\n            if (index === undefined) {\n                return 0;\n            }\n            const ttl = ttls[index];\n            const start = starts[index];\n            if (!ttl || !start) {\n                return Infinity;\n            }\n            const age = (cachedNow || getNow()) - start;\n            return ttl - age;\n        };\n        this.#isStale = index => {\n            const s = starts[index];\n            const t = ttls[index];\n            return !!t && !!s && (cachedNow || getNow()) - s > t;\n        };\n    }\n    // conditionally set private methods related to TTL\n    #updateItemAge = () => { };\n    #statusTTL = () => { };\n    #setItemTTL = () => { };\n    /* c8 ignore stop */\n    #isStale = () => false;\n    #initializeSizeTracking() {\n        const sizes = new ZeroArray(this.#max);\n        this.#calculatedSize = 0;\n        this.#sizes = sizes;\n        this.#removeItemSize = index => {\n            this.#calculatedSize -= sizes[index];\n            sizes[index] = 0;\n        };\n        this.#requireSize = (k, v, size, sizeCalculation) => {\n            // provisionally accept background fetches.\n            // actual value size will be checked when they return.\n            if (this.#isBackgroundFetch(v)) {\n                return 0;\n            }\n            if (!isPosInt(size)) {\n                if (sizeCalculation) {\n                    if (typeof sizeCalculation !== 'function') {\n                        throw new TypeError('sizeCalculation must be a function');\n                    }\n                    size = sizeCalculation(v, k);\n                    if (!isPosInt(size)) {\n                        throw new TypeError('sizeCalculation return invalid (expect positive integer)');\n                    }\n                }\n                else {\n                    throw new TypeError('invalid size value (must be positive integer). ' +\n                        'When maxSize or maxEntrySize is used, sizeCalculation ' +\n                        'or size must be set.');\n                }\n            }\n            return size;\n        };\n        this.#addItemSize = (index, size, status) => {\n            sizes[index] = size;\n            if (this.#maxSize) {\n                const maxSize = this.#maxSize - sizes[index];\n                while (this.#calculatedSize > maxSize) {\n                    this.#evict(true);\n                }\n            }\n            this.#calculatedSize += sizes[index];\n            if (status) {\n                status.entrySize = size;\n                status.totalCalculatedSize = this.#calculatedSize;\n            }\n        };\n    }\n    #removeItemSize = _i => { };\n    #addItemSize = (_i, _s, _st) => { };\n    #requireSize = (_k, _v, size, sizeCalculation) => {\n        if (size || sizeCalculation) {\n            throw new TypeError('cannot set size without setting maxSize or maxEntrySize on cache');\n        }\n        return 0;\n    };\n    *#indexes({ allowStale = this.allowStale } = {}) {\n        if (this.#size) {\n            for (let i = this.#tail; true;) {\n                if (!this.#isValidIndex(i)) {\n                    break;\n                }\n                if (allowStale || !this.#isStale(i)) {\n                    yield i;\n                }\n                if (i === this.#head) {\n                    break;\n                }\n                else {\n                    i = this.#prev[i];\n                }\n            }\n        }\n    }\n    *#rindexes({ allowStale = this.allowStale } = {}) {\n        if (this.#size) {\n            for (let i = this.#head; true;) {\n                if (!this.#isValidIndex(i)) {\n                    break;\n                }\n                if (allowStale || !this.#isStale(i)) {\n                    yield i;\n                }\n                if (i === this.#tail) {\n                    break;\n                }\n                else {\n                    i = this.#next[i];\n                }\n            }\n        }\n    }\n    #isValidIndex(index) {\n        return (index !== undefined &&\n            this.#keyMap.get(this.#keyList[index]) === index);\n    }\n    /**\n     * Return a generator yielding `[key, value]` pairs,\n     * in order from most recently used to least recently used.\n     */\n    *entries() {\n        for (const i of this.#indexes()) {\n            if (this.#valList[i] !== undefined &&\n                this.#keyList[i] !== undefined &&\n                !this.#isBackgroundFetch(this.#valList[i])) {\n                yield [this.#keyList[i], this.#valList[i]];\n            }\n        }\n    }\n    /**\n     * Inverse order version of {@link LRUCache.entries}\n     *\n     * Return a generator yielding `[key, value]` pairs,\n     * in order from least recently used to most recently used.\n     */\n    *rentries() {\n        for (const i of this.#rindexes()) {\n            if (this.#valList[i] !== undefined &&\n                this.#keyList[i] !== undefined &&\n                !this.#isBackgroundFetch(this.#valList[i])) {\n                yield [this.#keyList[i], this.#valList[i]];\n            }\n        }\n    }\n    /**\n     * Return a generator yielding the keys in the cache,\n     * in order from most recently used to least recently used.\n     */\n    *keys() {\n        for (const i of this.#indexes()) {\n            const k = this.#keyList[i];\n            if (k !== undefined &&\n                !this.#isBackgroundFetch(this.#valList[i])) {\n                yield k;\n            }\n        }\n    }\n    /**\n     * Inverse order version of {@link LRUCache.keys}\n     *\n     * Return a generator yielding the keys in the cache,\n     * in order from least recently used to most recently used.\n     */\n    *rkeys() {\n        for (const i of this.#rindexes()) {\n            const k = this.#keyList[i];\n            if (k !== undefined &&\n                !this.#isBackgroundFetch(this.#valList[i])) {\n                yield k;\n            }\n        }\n    }\n    /**\n     * Return a generator yielding the values in the cache,\n     * in order from most recently used to least recently used.\n     */\n    *values() {\n        for (const i of this.#indexes()) {\n            const v = this.#valList[i];\n            if (v !== undefined &&\n                !this.#isBackgroundFetch(this.#valList[i])) {\n                yield this.#valList[i];\n            }\n        }\n    }\n    /**\n     * Inverse order version of {@link LRUCache.values}\n     *\n     * Return a generator yielding the values in the cache,\n     * in order from least recently used to most recently used.\n     */\n    *rvalues() {\n        for (const i of this.#rindexes()) {\n            const v = this.#valList[i];\n            if (v !== undefined &&\n                !this.#isBackgroundFetch(this.#valList[i])) {\n                yield this.#valList[i];\n            }\n        }\n    }\n    /**\n     * Iterating over the cache itself yields the same results as\n     * {@link LRUCache.entries}\n     */\n    [Symbol.iterator]() {\n        return this.entries();\n    }\n    /**\n     * A String value that is used in the creation of the default string\n     * description of an object. Called by the built-in method\n     * `Object.prototype.toString`.\n     */\n    [Symbol.toStringTag] = 'LRUCache';\n    /**\n     * Find a value for which the supplied fn method returns a truthy value,\n     * similar to `Array.find()`. fn is called as `fn(value, key, cache)`.\n     */\n    find(fn, getOptions = {}) {\n        for (const i of this.#indexes()) {\n            const v = this.#valList[i];\n            const value = this.#isBackgroundFetch(v)\n                ? v.__staleWhileFetching\n                : v;\n            if (value === undefined)\n                continue;\n            if (fn(value, this.#keyList[i], this)) {\n                return this.get(this.#keyList[i], getOptions);\n            }\n        }\n    }\n    /**\n     * Call the supplied function on each item in the cache, in order from most\n     * recently used to least recently used.\n     *\n     * `fn` is called as `fn(value, key, cache)`.\n     *\n     * If `thisp` is provided, function will be called in the `this`-context of\n     * the provided object, or the cache if no `thisp` object is provided.\n     *\n     * Does not update age or recenty of use, or iterate over stale values.\n     */\n    forEach(fn, thisp = this) {\n        for (const i of this.#indexes()) {\n            const v = this.#valList[i];\n            const value = this.#isBackgroundFetch(v)\n                ? v.__staleWhileFetching\n                : v;\n            if (value === undefined)\n                continue;\n            fn.call(thisp, value, this.#keyList[i], this);\n        }\n    }\n    /**\n     * The same as {@link LRUCache.forEach} but items are iterated over in\n     * reverse order.  (ie, less recently used items are iterated over first.)\n     */\n    rforEach(fn, thisp = this) {\n        for (const i of this.#rindexes()) {\n            const v = this.#valList[i];\n            const value = this.#isBackgroundFetch(v)\n                ? v.__staleWhileFetching\n                : v;\n            if (value === undefined)\n                continue;\n            fn.call(thisp, value, this.#keyList[i], this);\n        }\n    }\n    /**\n     * Delete any stale entries. Returns true if anything was removed,\n     * false otherwise.\n     */\n    purgeStale() {\n        let deleted = false;\n        for (const i of this.#rindexes({ allowStale: true })) {\n            if (this.#isStale(i)) {\n                this.#delete(this.#keyList[i], 'expire');\n                deleted = true;\n            }\n        }\n        return deleted;\n    }\n    /**\n     * Get the extended info about a given entry, to get its value, size, and\n     * TTL info simultaneously. Returns `undefined` if the key is not present.\n     *\n     * Unlike {@link LRUCache#dump}, which is designed to be portable and survive\n     * serialization, the `start` value is always the current timestamp, and the\n     * `ttl` is a calculated remaining time to live (negative if expired).\n     *\n     * Always returns stale values, if their info is found in the cache, so be\n     * sure to check for expirations (ie, a negative {@link LRUCache.Entry#ttl})\n     * if relevant.\n     */\n    info(key) {\n        const i = this.#keyMap.get(key);\n        if (i === undefined)\n            return undefined;\n        const v = this.#valList[i];\n        const value = this.#isBackgroundFetch(v)\n            ? v.__staleWhileFetching\n            : v;\n        if (value === undefined)\n            return undefined;\n        const entry = { value };\n        if (this.#ttls && this.#starts) {\n            const ttl = this.#ttls[i];\n            const start = this.#starts[i];\n            if (ttl && start) {\n                const remain = ttl - (perf.now() - start);\n                entry.ttl = remain;\n                entry.start = Date.now();\n            }\n        }\n        if (this.#sizes) {\n            entry.size = this.#sizes[i];\n        }\n        return entry;\n    }\n    /**\n     * Return an array of [key, {@link LRUCache.Entry}] tuples which can be\n     * passed to {@link LRLUCache#load}.\n     *\n     * The `start` fields are calculated relative to a portable `Date.now()`\n     * timestamp, even if `performance.now()` is available.\n     *\n     * Stale entries are always included in the `dump`, even if\n     * {@link LRUCache.OptionsBase.allowStale} is false.\n     *\n     * Note: this returns an actual array, not a generator, so it can be more\n     * easily passed around.\n     */\n    dump() {\n        const arr = [];\n        for (const i of this.#indexes({ allowStale: true })) {\n            const key = this.#keyList[i];\n            const v = this.#valList[i];\n            const value = this.#isBackgroundFetch(v)\n                ? v.__staleWhileFetching\n                : v;\n            if (value === undefined || key === undefined)\n                continue;\n            const entry = { value };\n            if (this.#ttls && this.#starts) {\n                entry.ttl = this.#ttls[i];\n                // always dump the start relative to a portable timestamp\n                // it's ok for this to be a bit slow, it's a rare operation.\n                const age = perf.now() - this.#starts[i];\n                entry.start = Math.floor(Date.now() - age);\n            }\n            if (this.#sizes) {\n                entry.size = this.#sizes[i];\n            }\n            arr.unshift([key, entry]);\n        }\n        return arr;\n    }\n    /**\n     * Reset the cache and load in the items in entries in the order listed.\n     *\n     * The shape of the resulting cache may be different if the same options are\n     * not used in both caches.\n     *\n     * The `start` fields are assumed to be calculated relative to a portable\n     * `Date.now()` timestamp, even if `performance.now()` is available.\n     */\n    load(arr) {\n        this.clear();\n        for (const [key, entry] of arr) {\n            if (entry.start) {\n                // entry.start is a portable timestamp, but we may be using\n                // node's performance.now(), so calculate the offset, so that\n                // we get the intended remaining TTL, no matter how long it's\n                // been on ice.\n                //\n                // it's ok for this to be a bit slow, it's a rare operation.\n                const age = Date.now() - entry.start;\n                entry.start = perf.now() - age;\n            }\n            this.set(key, entry.value, entry);\n        }\n    }\n    /**\n     * Add a value to the cache.\n     *\n     * Note: if `undefined` is specified as a value, this is an alias for\n     * {@link LRUCache#delete}\n     *\n     * Fields on the {@link LRUCache.SetOptions} options param will override\n     * their corresponding values in the constructor options for the scope\n     * of this single `set()` operation.\n     *\n     * If `start` is provided, then that will set the effective start\n     * time for the TTL calculation. Note that this must be a previous\n     * value of `performance.now()` if supported, or a previous value of\n     * `Date.now()` if not.\n     *\n     * Options object may also include `size`, which will prevent\n     * calling the `sizeCalculation` function and just use the specified\n     * number if it is a positive integer, and `noDisposeOnSet` which\n     * will prevent calling a `dispose` function in the case of\n     * overwrites.\n     *\n     * If the `size` (or return value of `sizeCalculation`) for a given\n     * entry is greater than `maxEntrySize`, then the item will not be\n     * added to the cache.\n     *\n     * Will update the recency of the entry.\n     *\n     * If the value is `undefined`, then this is an alias for\n     * `cache.delete(key)`. `undefined` is never stored in the cache.\n     */\n    set(k, v, setOptions = {}) {\n        if (v === undefined) {\n            this.delete(k);\n            return this;\n        }\n        const { ttl = this.ttl, start, noDisposeOnSet = this.noDisposeOnSet, sizeCalculation = this.sizeCalculation, status, } = setOptions;\n        let { noUpdateTTL = this.noUpdateTTL } = setOptions;\n        const size = this.#requireSize(k, v, setOptions.size || 0, sizeCalculation);\n        // if the item doesn't fit, don't do anything\n        // NB: maxEntrySize set to maxSize by default\n        if (this.maxEntrySize && size > this.maxEntrySize) {\n            if (status) {\n                status.set = 'miss';\n                status.maxEntrySizeExceeded = true;\n            }\n            // have to delete, in case something is there already.\n            this.#delete(k, 'set');\n            return this;\n        }\n        let index = this.#size === 0 ? undefined : this.#keyMap.get(k);\n        if (index === undefined) {\n            // addition\n            index = (this.#size === 0\n                ? this.#tail\n                : this.#free.length !== 0\n                    ? this.#free.pop()\n                    : this.#size === this.#max\n                        ? this.#evict(false)\n                        : this.#size);\n            this.#keyList[index] = k;\n            this.#valList[index] = v;\n            this.#keyMap.set(k, index);\n            this.#next[this.#tail] = index;\n            this.#prev[index] = this.#tail;\n            this.#tail = index;\n            this.#size++;\n            this.#addItemSize(index, size, status);\n            if (status)\n                status.set = 'add';\n            noUpdateTTL = false;\n        }\n        else {\n            // update\n            this.#moveToTail(index);\n            const oldVal = this.#valList[index];\n            if (v !== oldVal) {\n                if (this.#hasFetchMethod && this.#isBackgroundFetch(oldVal)) {\n                    oldVal.__abortController.abort(new Error('replaced'));\n                    const { __staleWhileFetching: s } = oldVal;\n                    if (s !== undefined && !noDisposeOnSet) {\n                        if (this.#hasDispose) {\n                            this.#dispose?.(s, k, 'set');\n                        }\n                        if (this.#hasDisposeAfter) {\n                            this.#disposed?.push([s, k, 'set']);\n                        }\n                    }\n                }\n                else if (!noDisposeOnSet) {\n                    if (this.#hasDispose) {\n                        this.#dispose?.(oldVal, k, 'set');\n                    }\n                    if (this.#hasDisposeAfter) {\n                        this.#disposed?.push([oldVal, k, 'set']);\n                    }\n                }\n                this.#removeItemSize(index);\n                this.#addItemSize(index, size, status);\n                this.#valList[index] = v;\n                if (status) {\n                    status.set = 'replace';\n                    const oldValue = oldVal && this.#isBackgroundFetch(oldVal)\n                        ? oldVal.__staleWhileFetching\n                        : oldVal;\n                    if (oldValue !== undefined)\n                        status.oldValue = oldValue;\n                }\n            }\n            else if (status) {\n                status.set = 'update';\n            }\n        }\n        if (ttl !== 0 && !this.#ttls) {\n            this.#initializeTTLTracking();\n        }\n        if (this.#ttls) {\n            if (!noUpdateTTL) {\n                this.#setItemTTL(index, ttl, start);\n            }\n            if (status)\n                this.#statusTTL(status, index);\n        }\n        if (!noDisposeOnSet && this.#hasDisposeAfter && this.#disposed) {\n            const dt = this.#disposed;\n            let task;\n            while ((task = dt?.shift())) {\n                this.#disposeAfter?.(...task);\n            }\n        }\n        return this;\n    }\n    /**\n     * Evict the least recently used item, returning its value or\n     * `undefined` if cache is empty.\n     */\n    pop() {\n        try {\n            while (this.#size) {\n                const val = this.#valList[this.#head];\n                this.#evict(true);\n                if (this.#isBackgroundFetch(val)) {\n                    if (val.__staleWhileFetching) {\n                        return val.__staleWhileFetching;\n                    }\n                }\n                else if (val !== undefined) {\n                    return val;\n                }\n            }\n        }\n        finally {\n            if (this.#hasDisposeAfter && this.#disposed) {\n                const dt = this.#disposed;\n                let task;\n                while ((task = dt?.shift())) {\n                    this.#disposeAfter?.(...task);\n                }\n            }\n        }\n    }\n    #evict(free) {\n        const head = this.#head;\n        const k = this.#keyList[head];\n        const v = this.#valList[head];\n        if (this.#hasFetchMethod && this.#isBackgroundFetch(v)) {\n            v.__abortController.abort(new Error('evicted'));\n        }\n        else if (this.#hasDispose || this.#hasDisposeAfter) {\n            if (this.#hasDispose) {\n                this.#dispose?.(v, k, 'evict');\n            }\n            if (this.#hasDisposeAfter) {\n                this.#disposed?.push([v, k, 'evict']);\n            }\n        }\n        this.#removeItemSize(head);\n        // if we aren't about to use the index, then null these out\n        if (free) {\n            this.#keyList[head] = undefined;\n            this.#valList[head] = undefined;\n            this.#free.push(head);\n        }\n        if (this.#size === 1) {\n            this.#head = this.#tail = 0;\n            this.#free.length = 0;\n        }\n        else {\n            this.#head = this.#next[head];\n        }\n        this.#keyMap.delete(k);\n        this.#size--;\n        return head;\n    }\n    /**\n     * Check if a key is in the cache, without updating the recency of use.\n     * Will return false if the item is stale, even though it is technically\n     * in the cache.\n     *\n     * Check if a key is in the cache, without updating the recency of\n     * use. Age is updated if {@link LRUCache.OptionsBase.updateAgeOnHas} is set\n     * to `true` in either the options or the constructor.\n     *\n     * Will return `false` if the item is stale, even though it is technically in\n     * the cache. The difference can be determined (if it matters) by using a\n     * `status` argument, and inspecting the `has` field.\n     *\n     * Will not update item age unless\n     * {@link LRUCache.OptionsBase.updateAgeOnHas} is set.\n     */\n    has(k, hasOptions = {}) {\n        const { updateAgeOnHas = this.updateAgeOnHas, status } = hasOptions;\n        const index = this.#keyMap.get(k);\n        if (index !== undefined) {\n            const v = this.#valList[index];\n            if (this.#isBackgroundFetch(v) &&\n                v.__staleWhileFetching === undefined) {\n                return false;\n            }\n            if (!this.#isStale(index)) {\n                if (updateAgeOnHas) {\n                    this.#updateItemAge(index);\n                }\n                if (status) {\n                    status.has = 'hit';\n                    this.#statusTTL(status, index);\n                }\n                return true;\n            }\n            else if (status) {\n                status.has = 'stale';\n                this.#statusTTL(status, index);\n            }\n        }\n        else if (status) {\n            status.has = 'miss';\n        }\n        return false;\n    }\n    /**\n     * Like {@link LRUCache#get} but doesn't update recency or delete stale\n     * items.\n     *\n     * Returns `undefined` if the item is stale, unless\n     * {@link LRUCache.OptionsBase.allowStale} is set.\n     */\n    peek(k, peekOptions = {}) {\n        const { allowStale = this.allowStale } = peekOptions;\n        const index = this.#keyMap.get(k);\n        if (index === undefined ||\n            (!allowStale && this.#isStale(index))) {\n            return;\n        }\n        const v = this.#valList[index];\n        // either stale and allowed, or forcing a refresh of non-stale value\n        return this.#isBackgroundFetch(v) ? v.__staleWhileFetching : v;\n    }\n    #backgroundFetch(k, index, options, context) {\n        const v = index === undefined ? undefined : this.#valList[index];\n        if (this.#isBackgroundFetch(v)) {\n            return v;\n        }\n        const ac = new AC();\n        const { signal } = options;\n        // when/if our AC signals, then stop listening to theirs.\n        signal?.addEventListener('abort', () => ac.abort(signal.reason), {\n            signal: ac.signal,\n        });\n        const fetchOpts = {\n            signal: ac.signal,\n            options,\n            context,\n        };\n        const cb = (v, updateCache = false) => {\n            const { aborted } = ac.signal;\n            const ignoreAbort = options.ignoreFetchAbort && v !== undefined;\n            if (options.status) {\n                if (aborted && !updateCache) {\n                    options.status.fetchAborted = true;\n                    options.status.fetchError = ac.signal.reason;\n                    if (ignoreAbort)\n                        options.status.fetchAbortIgnored = true;\n                }\n                else {\n                    options.status.fetchResolved = true;\n                }\n            }\n            if (aborted && !ignoreAbort && !updateCache) {\n                return fetchFail(ac.signal.reason);\n            }\n            // either we didn't abort, and are still here, or we did, and ignored\n            const bf = p;\n            if (this.#valList[index] === p) {\n                if (v === undefined) {\n                    if (bf.__staleWhileFetching) {\n                        this.#valList[index] = bf.__staleWhileFetching;\n                    }\n                    else {\n                        this.#delete(k, 'fetch');\n                    }\n                }\n                else {\n                    if (options.status)\n                        options.status.fetchUpdated = true;\n                    this.set(k, v, fetchOpts.options);\n                }\n            }\n            return v;\n        };\n        const eb = (er) => {\n            if (options.status) {\n                options.status.fetchRejected = true;\n                options.status.fetchError = er;\n            }\n            return fetchFail(er);\n        };\n        const fetchFail = (er) => {\n            const { aborted } = ac.signal;\n            const allowStaleAborted = aborted && options.allowStaleOnFetchAbort;\n            const allowStale = allowStaleAborted || options.allowStaleOnFetchRejection;\n            const noDelete = allowStale || options.noDeleteOnFetchRejection;\n            const bf = p;\n            if (this.#valList[index] === p) {\n                // if we allow stale on fetch rejections, then we need to ensure that\n                // the stale value is not removed from the cache when the fetch fails.\n                const del = !noDelete || bf.__staleWhileFetching === undefined;\n                if (del) {\n                    this.#delete(k, 'fetch');\n                }\n                else if (!allowStaleAborted) {\n                    // still replace the *promise* with the stale value,\n                    // since we are done with the promise at this point.\n                    // leave it untouched if we're still waiting for an\n                    // aborted background fetch that hasn't yet returned.\n                    this.#valList[index] = bf.__staleWhileFetching;\n                }\n            }\n            if (allowStale) {\n                if (options.status && bf.__staleWhileFetching !== undefined) {\n                    options.status.returnedStale = true;\n                }\n                return bf.__staleWhileFetching;\n            }\n            else if (bf.__returned === bf) {\n                throw er;\n            }\n        };\n        const pcall = (res, rej) => {\n            const fmp = this.#fetchMethod?.(k, v, fetchOpts);\n            if (fmp && fmp instanceof Promise) {\n                fmp.then(v => res(v === undefined ? undefined : v), rej);\n            }\n            // ignored, we go until we finish, regardless.\n            // defer check until we are actually aborting,\n            // so fetchMethod can override.\n            ac.signal.addEventListener('abort', () => {\n                if (!options.ignoreFetchAbort ||\n                    options.allowStaleOnFetchAbort) {\n                    res(undefined);\n                    // when it eventually resolves, update the cache.\n                    if (options.allowStaleOnFetchAbort) {\n                        res = v => cb(v, true);\n                    }\n                }\n            });\n        };\n        if (options.status)\n            options.status.fetchDispatched = true;\n        const p = new Promise(pcall).then(cb, eb);\n        const bf = Object.assign(p, {\n            __abortController: ac,\n            __staleWhileFetching: v,\n            __returned: undefined,\n        });\n        if (index === undefined) {\n            // internal, don't expose status.\n            this.set(k, bf, { ...fetchOpts.options, status: undefined });\n            index = this.#keyMap.get(k);\n        }\n        else {\n            this.#valList[index] = bf;\n        }\n        return bf;\n    }\n    #isBackgroundFetch(p) {\n        if (!this.#hasFetchMethod)\n            return false;\n        const b = p;\n        return (!!b &&\n            b instanceof Promise &&\n            b.hasOwnProperty('__staleWhileFetching') &&\n            b.__abortController instanceof AC);\n    }\n    async fetch(k, fetchOptions = {}) {\n        const { \n        // get options\n        allowStale = this.allowStale, updateAgeOnGet = this.updateAgeOnGet, noDeleteOnStaleGet = this.noDeleteOnStaleGet, \n        // set options\n        ttl = this.ttl, noDisposeOnSet = this.noDisposeOnSet, size = 0, sizeCalculation = this.sizeCalculation, noUpdateTTL = this.noUpdateTTL, \n        // fetch exclusive options\n        noDeleteOnFetchRejection = this.noDeleteOnFetchRejection, allowStaleOnFetchRejection = this.allowStaleOnFetchRejection, ignoreFetchAbort = this.ignoreFetchAbort, allowStaleOnFetchAbort = this.allowStaleOnFetchAbort, context, forceRefresh = false, status, signal, } = fetchOptions;\n        if (!this.#hasFetchMethod) {\n            if (status)\n                status.fetch = 'get';\n            return this.get(k, {\n                allowStale,\n                updateAgeOnGet,\n                noDeleteOnStaleGet,\n                status,\n            });\n        }\n        const options = {\n            allowStale,\n            updateAgeOnGet,\n            noDeleteOnStaleGet,\n            ttl,\n            noDisposeOnSet,\n            size,\n            sizeCalculation,\n            noUpdateTTL,\n            noDeleteOnFetchRejection,\n            allowStaleOnFetchRejection,\n            allowStaleOnFetchAbort,\n            ignoreFetchAbort,\n            status,\n            signal,\n        };\n        let index = this.#keyMap.get(k);\n        if (index === undefined) {\n            if (status)\n                status.fetch = 'miss';\n            const p = this.#backgroundFetch(k, index, options, context);\n            return (p.__returned = p);\n        }\n        else {\n            // in cache, maybe already fetching\n            const v = this.#valList[index];\n            if (this.#isBackgroundFetch(v)) {\n                const stale = allowStale && v.__staleWhileFetching !== undefined;\n                if (status) {\n                    status.fetch = 'inflight';\n                    if (stale)\n                        status.returnedStale = true;\n                }\n                return stale ? v.__staleWhileFetching : (v.__returned = v);\n            }\n            // if we force a refresh, that means do NOT serve the cached value,\n            // unless we are already in the process of refreshing the cache.\n            const isStale = this.#isStale(index);\n            if (!forceRefresh && !isStale) {\n                if (status)\n                    status.fetch = 'hit';\n                this.#moveToTail(index);\n                if (updateAgeOnGet) {\n                    this.#updateItemAge(index);\n                }\n                if (status)\n                    this.#statusTTL(status, index);\n                return v;\n            }\n            // ok, it is stale or a forced refresh, and not already fetching.\n            // refresh the cache.\n            const p = this.#backgroundFetch(k, index, options, context);\n            const hasStale = p.__staleWhileFetching !== undefined;\n            const staleVal = hasStale && allowStale;\n            if (status) {\n                status.fetch = isStale ? 'stale' : 'refresh';\n                if (staleVal && isStale)\n                    status.returnedStale = true;\n            }\n            return staleVal ? p.__staleWhileFetching : (p.__returned = p);\n        }\n    }\n    async forceFetch(k, fetchOptions = {}) {\n        const v = await this.fetch(k, fetchOptions);\n        if (v === undefined)\n            throw new Error('fetch() returned undefined');\n        return v;\n    }\n    memo(k, memoOptions = {}) {\n        const memoMethod = this.#memoMethod;\n        if (!memoMethod) {\n            throw new Error('no memoMethod provided to constructor');\n        }\n        const { context, forceRefresh, ...options } = memoOptions;\n        const v = this.get(k, options);\n        if (!forceRefresh && v !== undefined)\n            return v;\n        const vv = memoMethod(k, v, {\n            options,\n            context,\n        });\n        this.set(k, vv, options);\n        return vv;\n    }\n    /**\n     * Return a value from the cache. Will update the recency of the cache\n     * entry found.\n     *\n     * If the key is not found, get() will return `undefined`.\n     */\n    get(k, getOptions = {}) {\n        const { allowStale = this.allowStale, updateAgeOnGet = this.updateAgeOnGet, noDeleteOnStaleGet = this.noDeleteOnStaleGet, status, } = getOptions;\n        const index = this.#keyMap.get(k);\n        if (index !== undefined) {\n            const value = this.#valList[index];\n            const fetching = this.#isBackgroundFetch(value);\n            if (status)\n                this.#statusTTL(status, index);\n            if (this.#isStale(index)) {\n                if (status)\n                    status.get = 'stale';\n                // delete only if not an in-flight background fetch\n                if (!fetching) {\n                    if (!noDeleteOnStaleGet) {\n                        this.#delete(k, 'expire');\n                    }\n                    if (status && allowStale)\n                        status.returnedStale = true;\n                    return allowStale ? value : undefined;\n                }\n                else {\n                    if (status &&\n                        allowStale &&\n                        value.__staleWhileFetching !== undefined) {\n                        status.returnedStale = true;\n                    }\n                    return allowStale ? value.__staleWhileFetching : undefined;\n                }\n            }\n            else {\n                if (status)\n                    status.get = 'hit';\n                // if we're currently fetching it, we don't actually have it yet\n                // it's not stale, which means this isn't a staleWhileRefetching.\n                // If it's not stale, and fetching, AND has a __staleWhileFetching\n                // value, then that means the user fetched with {forceRefresh:true},\n                // so it's safe to return that value.\n                if (fetching) {\n                    return value.__staleWhileFetching;\n                }\n                this.#moveToTail(index);\n                if (updateAgeOnGet) {\n                    this.#updateItemAge(index);\n                }\n                return value;\n            }\n        }\n        else if (status) {\n            status.get = 'miss';\n        }\n    }\n    #connect(p, n) {\n        this.#prev[n] = p;\n        this.#next[p] = n;\n    }\n    #moveToTail(index) {\n        // if tail already, nothing to do\n        // if head, move head to next[index]\n        // else\n        //   move next[prev[index]] to next[index] (head has no prev)\n        //   move prev[next[index]] to prev[index]\n        // prev[index] = tail\n        // next[tail] = index\n        // tail = index\n        if (index !== this.#tail) {\n            if (index === this.#head) {\n                this.#head = this.#next[index];\n            }\n            else {\n                this.#connect(this.#prev[index], this.#next[index]);\n            }\n            this.#connect(this.#tail, index);\n            this.#tail = index;\n        }\n    }\n    /**\n     * Deletes a key out of the cache.\n     *\n     * Returns true if the key was deleted, false otherwise.\n     */\n    delete(k) {\n        return this.#delete(k, 'delete');\n    }\n    #delete(k, reason) {\n        let deleted = false;\n        if (this.#size !== 0) {\n            const index = this.#keyMap.get(k);\n            if (index !== undefined) {\n                deleted = true;\n                if (this.#size === 1) {\n                    this.#clear(reason);\n                }\n                else {\n                    this.#removeItemSize(index);\n                    const v = this.#valList[index];\n                    if (this.#isBackgroundFetch(v)) {\n                        v.__abortController.abort(new Error('deleted'));\n                    }\n                    else if (this.#hasDispose || this.#hasDisposeAfter) {\n                        if (this.#hasDispose) {\n                            this.#dispose?.(v, k, reason);\n                        }\n                        if (this.#hasDisposeAfter) {\n                            this.#disposed?.push([v, k, reason]);\n                        }\n                    }\n                    this.#keyMap.delete(k);\n                    this.#keyList[index] = undefined;\n                    this.#valList[index] = undefined;\n                    if (index === this.#tail) {\n                        this.#tail = this.#prev[index];\n                    }\n                    else if (index === this.#head) {\n                        this.#head = this.#next[index];\n                    }\n                    else {\n                        const pi = this.#prev[index];\n                        this.#next[pi] = this.#next[index];\n                        const ni = this.#next[index];\n                        this.#prev[ni] = this.#prev[index];\n                    }\n                    this.#size--;\n                    this.#free.push(index);\n                }\n            }\n        }\n        if (this.#hasDisposeAfter && this.#disposed?.length) {\n            const dt = this.#disposed;\n            let task;\n            while ((task = dt?.shift())) {\n                this.#disposeAfter?.(...task);\n            }\n        }\n        return deleted;\n    }\n    /**\n     * Clear the cache entirely, throwing away all values.\n     */\n    clear() {\n        return this.#clear('delete');\n    }\n    #clear(reason) {\n        for (const index of this.#rindexes({ allowStale: true })) {\n            const v = this.#valList[index];\n            if (this.#isBackgroundFetch(v)) {\n                v.__abortController.abort(new Error('deleted'));\n            }\n            else {\n                const k = this.#keyList[index];\n                if (this.#hasDispose) {\n                    this.#dispose?.(v, k, reason);\n                }\n                if (this.#hasDisposeAfter) {\n                    this.#disposed?.push([v, k, reason]);\n                }\n            }\n        }\n        this.#keyMap.clear();\n        this.#valList.fill(undefined);\n        this.#keyList.fill(undefined);\n        if (this.#ttls && this.#starts) {\n            this.#ttls.fill(0);\n            this.#starts.fill(0);\n        }\n        if (this.#sizes) {\n            this.#sizes.fill(0);\n        }\n        this.#head = 0;\n        this.#tail = 0;\n        this.#free.length = 0;\n        this.#calculatedSize = 0;\n        this.#size = 0;\n        if (this.#hasDisposeAfter && this.#disposed) {\n            const dt = this.#disposed;\n            let task;\n            while ((task = dt?.shift())) {\n                this.#disposeAfter?.(...task);\n            }\n        }\n    }\n}\n//# sourceMappingURL=index.js.map","import {LRUCache}from'lru-cache';var P=class extends Error{constructor(e,t,n){super(t),this.name=\"HwError\",this.code=e,n!==void 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'${n}'`});let o=i.monomerType;o===void 0?t.push({path:`${e}.monomerType`,message:\"Required property missing\"}):typeof o!=\"string\"?t.push({path:`${e}.monomerType`,message:`Expected string, got ${G(o)}`}):ur.has(o)||t.push({path:`${e}.monomerType`,message:`Expected one of Backbone|Branch|Terminal|Undefined, got '${o}'`});let r=i.rgroups;if(r===void 0)t.push({path:`${e}.rgroups`,message:\"Required property missing\"});else if(!Array.isArray(r))t.push({path:`${e}.rgroups`,message:`Expected array, got ${G(r)}`});else {let s=new Set;for(let a=0;a<r.length;a++)hr(r[a],`${e}.rgroups[${a}]`,t,s);}if(tt(i,\"name\",e,t),tt(i,\"smiles\",e,t),tt(i,\"naturalAnalog\",e,t),tt(i,\"author\",e,t),\"createDate\"in i&&i.createDate!==void 0&&i.createDate!==null&&typeof i.createDate!=\"string\"&&t.push({path:`${e}.createDate`,message:`Expected string or null, got ${G(i.createDate)}`}),\"id\"in i&&i.id!==void 0){let s=i.id;typeof s==\"string\"||typeof s==\"number\"&&Number.isInteger(s)||t.push({path:`${e}.id`,message:`Expected integer or string, got ${G(s)}`});}if(\"meta\"in i&&i.meta!==void 0){let s=i.meta;nt(s)?s.colors!==void 0&&fr(s.colors,`${e}.meta.colors`,t):t.push({path:`${e}.meta`,message:`Expected object, got ${G(s)}`});}}function hr(i,e,t,n){if(!nt(i)){t.push({path:e,message:`Expected an object, got ${G(i)}`});return}let o=i.label;if(o===void 0?t.push({path:`${e}.label`,message:\"Required property missing\"}):typeof o!=\"string\"?t.push({path:`${e}.label`,message:`Expected string, got ${G(o)}`}):mr.test(o)?n.has(o)?t.push({path:`${e}.label`,message:`Duplicate R-group label '${o}'`}):n.add(o):t.push({path:`${e}.label`,message:`Expected pattern /^R[1-9][0-9]*$/, got '${o}'`}),pn(i,\"capGroupName\",e,t),et(i)===void 0){let r=Object.keys(i).some(s=>s.toLowerCase()===\"capgroupsmiles\");t.push({path:`${e}.capGroupSMILES`,message:r?\"Expected string\":\"Required property missing\"});}tt(i,\"alternateId\",e,t),\"id\"in i&&i.id!==void 0&&(typeof i.id!=\"number\"||!Number.isInteger(i.id))&&t.push({path:`${e}.id`,message:`Expected integer, got ${G(i.id)}`});}function fr(i,e,t){if(!nt(i)){t.push({path:e,message:`Expected object, got ${G(i)}`});return}for(let n of [\"default\",\"light\",\"dark\"])i[n]!==void 0&&br(i[n],`${e}.${n}`,t);}function br(i,e,t){if(!nt(i)){t.push({path:e,message:`Expected object, got ${G(i)}`});return}for(let n of [\"line\",\"text\",\"background\"])i[n]===void 0?t.push({path:`${e}.${n}`,message:\"Required property missing\"}):typeof i[n]!=\"string\"&&t.push({path:`${e}.${n}`,message:`Expected string, got ${G(i[n])}`});}function pn(i,e,t,n,o){let r=i[e],s=`${t}.${e}`;if(r===void 0){n.push({path:s,message:\"Required property missing\"});return}if(typeof r!=\"string\"){n.push({path:s,message:`Expected string, got ${G(r)}`});return}o?.minLength!==void 0&&r.length<o.minLength&&n.push({path:s,message:`Expected string of length >= ${o.minLength}, got ${r.length}`});}function tt(i,e,t,n){let o=i[e];o!==void 0&&typeof o!=\"string\"&&n.push({path:`${t}.${e}`,message:`Expected string, got ${G(o)}`});}function nt(i){return typeof i==\"object\"&&i!==null&&!Array.isArray(i)}function G(i){return i===null?\"null\":Array.isArray(i)?\"array\":typeof i}var yr=/^R([1-9][0-9]*)$/;function te(i){switch(i.polymerType){case x.PEPTIDE:return g.AA;case x.CHEM:return g.CHEM;case x.BLOB:return g.BLOB;case x.RNA:{if(i.monomerType===\"Branch\")return g.BASE;if(i.monomerType===\"Backbone\"){let e=i.naturalAnalog;return e===\"P\"||e===\"p\"?g.LINKER:g.SUGAR}return null}default:return null}}function gr(i){let e=new Map;for(let t of i.rgroups){let n=yr.exec(t.label);n!==null&&e.set(parseInt(n[1],10),t);}return Object.assign({},i,{rs:i.rgroups.length,rgroupMap:e})}var hn=class i{constructor(e){this._version=0;this._byPolymerSymbol=new Map;this._byBiotypeSymbol=new Map;this._byNaturalAnalog=new Map;this._resolved=new WeakMap;this._inlineSmilesCounter=0;this.source=e,this.onChanged=new Z;}static empty(e=\"empty\"){return new i(e)}static fromJSON(e,t=\"inline\",n){let o=new i(t);for(let r=0;r<e.length;r++){let s=e[r],a=Mt([s]);if(!a.ok){n!==void 0?n.skipped.push({index:r,errors:a.errors}):console.warn(`MonomerLib.fromJSON: skipping invalid entry at index ${r}`,a.errors);continue}o._addNoFire(s);}return o}static fromText(e,t=\"inline\"){let n;try{n=JSON.parse(e);}catch(r){let s=r instanceof Error?r.message:String(r);throw new P(\"invalid-monomer-lib\",`MonomerLib.fromText: JSON.parse failed \\u2014 ${s}`)}let o=Mt(n);if(!o.ok)throw new P(\"invalid-monomer-lib\",`MonomerLib.fromText: schema validation failed (${o.errors.length} errors)`,{errors:o.errors});return i.fromJSON(o.data,t)}static async fromUrl(e,t){let n=t??globalThis.fetch;if(n===void 0)throw new P(\"fetch-unavailable\",\"MonomerLib.fromUrl: no fetch implementation available \\u2014 pass `fetchImpl` or run in a fetch-capable environment.\",{url:e});let o=await n(e);if(!o.ok)throw new P(\"monomer-lib-fetch-failed\",`MonomerLib.fromUrl: HTTP ${o.status} fetching ${e}`,{url:e,status:o.status});let r=await o.text();return i.fromText(r,e)}static merge(...e){let t=e.map(o=>o.source).join(\"+\")||\"empty\",n=new i(t);for(let o of e)for(let r of o.getPolymerTypes())for(let s of o.getMonomerSymbolsByType(r)){let a=o.getMonomer(r,s);a!==null&&n._addNoFire(a);}return n}get isEmpty(){for(let e of this._byPolymerSymbol.values())if(e.size>0)return  false;return  true}get version(){return this._version}getMonomer(e,t){let n=this._byPolymerSymbol.get(e);return n===void 0?null:n.get(t)??null}getMonomerSet(e){let t=this._byBiotypeSymbol.get(e);return t===void 0?new Map:new Map(t)}getMonomerSymbolsByType(e){let t=this._byPolymerSymbol.get(e);return t===void 0?[]:Array.from(t.keys())}getByNaturalAnalog(e,t){let n=this._byNaturalAnalog.get(e);if(n===void 0)return [];let o=n.get(t);return o===void 0?[]:o.slice()}getPolymerTypes(){let e=[];for(let[t,n]of this._byPolymerSymbol.entries())n.size>0&&e.push(t);return e}getColors(e,t){let n=_r(t),o=e===null?g.AA:te(e)??g.AA;return D(e,o,n)}getResolved(e){return this._resolved.get(e)}addMonomer(e){let t=Mt([e]);if(!t.ok)throw new P(\"invalid-monomer\",\"MonomerLib.addMonomer: schema validation failed\",{errors:t.errors});let n=this._addNoFire(e);this._bumpVersion(),this.onChanged.next({type:n?\"update\":\"add\",affectedSymbols:[e.symbol]});}addMonomers(e){let t=[],n=false;for(let o of e)this._addNoFire(o)&&(n=true),t.push(o.symbol);t.length!==0&&(this._bumpVersion(),this.onChanged.next({type:n?\"update\":\"add\",affectedSymbols:t}));}removeMonomer(e,t){let n=this._byPolymerSymbol.get(e);if(n===void 0)return  false;let o=n.get(t);if(o===void 0)return  false;n.delete(t);let r=te(o);if(r!==null){let a=this._byBiotypeSymbol.get(r);a!==void 0&&a.delete(t);}let s=o.naturalAnalog;if(s!==void 0&&s!==\"\"){let d=this._byNaturalAnalog.get(e)?.get(s);if(d!==void 0){let l=d.indexOf(o);l>=0&&d.splice(l,1);}}return this._bumpVersion(),this.onChanged.next({type:\"remove\",affectedSymbols:[t]}),true}setMonomerColors(e,t,n){let o=this.getMonomer(e,t);if(o===null)throw new P(\"monomer-not-found\",`MonomerLib.setMonomerColors: ${e}/${t} not found`,{polymerType:e,symbol:t});let r=o.meta??{},s=r.colors??{},a=Object.assign({},r,{colors:Object.assign({},s,n)}),d=Object.assign({},o,{meta:a});this._addNoFire(d),this._bumpVersion(),this.onChanged.next({type:\"update\",affectedSymbols:[t]});}merge(e){for(let t of e.getPolymerTypes())for(let n of e.getMonomerSymbolsByType(t)){let o=e.getMonomer(t,n);o!==null&&this._addNoFire(o);}this._bumpVersion(),this.onChanged.next({type:\"reload\"});}registerInlineSmilesMonomer(e,t,n){let o=no(t);if(!o.ok)throw new P(\"inline-smiles-without-r-groups\",`MonomerLib.registerInlineSmilesMonomer: ${o.reason}`,{smiles:t});this._inlineSmilesCounter+=1;let r=`#${this._inlineSmilesCounter}`,s=[],a=Array.from(o.info.rgroupPositions.keys()).sort((u,c)=>u-c);for(let u of a)s.push({label:`R${u}`,capGroupName:\"H\",capGroupSMILES:\"\"});let d=n?.symbolHint!==void 0?{smilesHint:n.symbolHint}:void 0,l={symbol:r,polymerType:e,monomerType:\"Undefined\",molfile:\"\",smiles:o.canonicalSmiles,rgroups:s,...d!==void 0?{meta:d}:{}};return this._addNoFire(l),this._bumpVersion(),this.onChanged.next({type:\"add\",affectedSymbols:[r]}),l}toJSON(){let e=[];for(let t of this._byPolymerSymbol.values())for(let n of t.values())e.push(n);return e}_addNoFire(e){e=fo(e);let t=e.polymerType,n=this._byPolymerSymbol.get(t);n===void 0&&(n=new Map,this._byPolymerSymbol.set(t,n));let o=n.get(e.symbol);if(n.set(e.symbol,e),o!==void 0){let a=te(o);if(a!==null){let l=this._byBiotypeSymbol.get(a);l!==void 0&&l.delete(o.symbol);}let d=o.naturalAnalog;if(d!==void 0&&d!==\"\"){let l=this._byNaturalAnalog.get(t)?.get(d);if(l!==void 0){let u=l.indexOf(o);u>=0&&l.splice(u,1);}}this._resolved.delete(o);}let r=te(e);if(r!==null){let a=this._byBiotypeSymbol.get(r);a===void 0&&(a=new Map,this._byBiotypeSymbol.set(r,a)),a.set(e.symbol,e);}let s=e.naturalAnalog;if(s!==void 0&&s!==\"\"){let a=this._byNaturalAnalog.get(t);a===void 0&&(a=new Map,this._byNaturalAnalog.set(t,a));let d=a.get(s);d===void 0&&(d=[],a.set(s,d)),d.push(e);}return this._resolved.set(e,gr(e)),o!==void 0}_bumpVersion(){this._version+=1;}};function _r(i){return i===\"dark\"?Ie:we}function ke(i,e,t){return new fn(i,e,t??{}).run()}var vr=new Set([\"?\",\"*\",\"_\",\"X\",\"N\"]),xr=/^R([1-9][0-9]*)$/;function wr(i){return typeof i.registerInlineSmilesMonomer==\"function\"}var fn=class{constructor(e,t,n){this.diagnostics=[];this.oldToNew=new Map;this.placeholderCache=new Map;this.mol=e,this.lib=t,this.options=n;}run(){let e=new Map;for(let a of this.mol.chains)e.set(a.id,a.polymerType);for(let a of this.mol.atoms){let d=e.get(a.bio.chainId)??null,l=this.resolveAtom(a,d);this.oldToNew.set(a.id,l);}for(let a of this.mol.atoms){let d=this.oldToNew.get(a.id);if(d===void 0||a.branchAtom===void 0)continue;let l=this.oldToNew.get(a.branchAtom.id);l!==void 0&&(d.branchAtom=l);}let t=[];for(let a of this.mol.bonds){let d=this.oldToNew.get(a.a1.id),l=this.oldToNew.get(a.a2.id);d===void 0||l===void 0||t.push({...a,a1:d,a2:l});}let n=new Map;for(let a of t)n.set(a.id,a);let o=[];for(let a of this.mol.chains){let d=[];for(let u of a.backboneAtoms){let c=this.oldToNew.get(u.id);c!==void 0&&d.push(c);}let l=[];for(let u of a.bonds){let c=n.get(u.id);c!==void 0&&l.push(c);}o.push({id:a.id,polymerType:a.polymerType,backboneAtoms:d,bonds:l,...a.annotation!==void 0?{annotation:a.annotation}:{},...a.strandType!==void 0?{strandType:a.strandType}:{}});}return {mol:{atoms:this.mol.atoms.map(a=>this.oldToNew.get(a.id)),bonds:t,chains:o,groups:this.mol.groups,annotations:this.mol.annotations},diagnostics:this.diagnostics}}resolveAtom(e,t){let n=null,o=e.biotype;if(t!==null){let r=this.lib.getMonomer(t,e.symbol);if(r!==null)n=this.toResolved(r),o=te(r)??e.biotype;else if(this.isAmbiguitySymbol(e))n=this.synthesizeAmbiguity(t,e),this.emit(\"info\",\"ambiguous-monomer\",`Ambiguous monomer '${e.symbol}' on chain '${e.bio.chainId}'`,e);else if(Be(e.symbol))n=this.registerInlineSmilesFallback(t,e);else if(this.options.legacyCaseFallback===true&&t===\"RNA\"){let s=this.findCaseInsensitiveMatch(t,e.symbol);s!==null&&(n=this.toResolved(s),o=te(s)??e.biotype,this.emit(\"info\",\"case-mismatch\",`Symbol '${e.symbol}' matched library entry '${s.symbol}' only after case fold`,e));}n===null&&(n=this.synthesizeMissing(t,e),this.emit(\"warning\",\"unresolved-monomer\",`Monomer '${e.symbol}' not found in library for ${t}`,e));}return {...e,monomer:n,biotype:o}}toResolved(e){let t=this.lib.getResolved?.(e);if(t!==void 0)return t;let n=new Map;for(let o of e.rgroups){let r=xr.exec(o.label);r!==null&&n.set(parseInt(r[1],10),o);}return Object.assign({},e,{rs:e.rgroups.length,rgroupMap:n})}isAmbiguitySymbol(e){return !!(vr.has(e.symbol)||e.bio.ambiguity!==void 0)}synthesizeAmbiguity(e,t){let n=`ambig:${e}:${t.symbol}`,o=this.placeholderCache.get(n);return o===void 0&&(o={symbol:t.symbol,polymerType:e,monomerType:\"Undefined\",molfile:\"\",rgroups:[{label:\"R1\",capGroupName:\"H\",capGroupSMILES:\"\"},{label:\"R2\",capGroupName:\"H\",capGroupSMILES:\"\"}],meta:{ambiguous:true}},this.placeholderCache.set(n,o)),this.toResolved(o)}synthesizeMissing(e,t){let n=`missing:${e}:${t.symbol}`,o=this.placeholderCache.get(n);return o===void 0&&(o={symbol:t.symbol,polymerType:e,monomerType:\"Undefined\",molfile:\"\",rgroups:[{label:\"R1\",capGroupName:\"H\",capGroupSMILES:\"\"},{label:\"R2\",capGroupName:\"H\",capGroupSMILES:\"\"}],meta:{missing:true}},this.placeholderCache.set(n,o)),this.toResolved(o)}registerInlineSmilesFallback(e,t){if(wr(this.lib))try{let n=this.lib.registerInlineSmilesMonomer(e,t.symbol);return this.toResolved(n)}catch{this.emit(\"warning\",\"inline-smiles-without-r-groups\",`Inline SMILES '${kr(t.symbol,40)}' has no detectable R-groups`,t);}else this.emit(\"warning\",\"inline-smiles-without-r-groups\",\"Inline SMILES seen but lib has no registerInlineSmilesMonomer\",t);return this.synthesizeMissing(e,t)}findCaseInsensitiveMatch(e,t){let n=t.toLowerCase();for(let o of this.lib.getMonomerSymbolsByType(e))if(o.toLowerCase()===n&&o!==t){let r=this.lib.getMonomer(e,o);if(r!==null)return r}return null}emit(e,t,n,o){let r={chainId:o.bio.chainId,atomId:o.id,symbol:o.symbol};this.diagnostics.push({severity:e,code:t,message:n,context:r});}};function kr(i,e){return i.length<=e?i:i.slice(0,e-1)+\"\\u2026\"}function ot(i,e,t){let n=t?.mode??\"lenient\",o;try{o=to(i);}catch(r){if(r instanceof F){if(n===\"strict\")throw r;let s={severity:\"error\",code:r.code,message:r.message,...r.span!==void 0?{span:{start:r.span.start,end:r.span.end}}:{}};return {mol:me(),diagnostics:[s]}}throw r}return yo(o,e,t)}function yo(i,e,t){let o=new yn(i,e,t?.mode??\"lenient\").parseDocument();if(e===null||t?.resolveMonomers===false)return o;let r=ke(o.mol,e,{mode:t?.mode??\"lenient\",...t?.legacyCaseFallback===true?{legacyCaseFallback:true}:{}});return {mol:r.mol,diagnostics:[...o.diagnostics,...r.diagnostics]}}var bn=class{constructor(e){this.tokens=e.tokens,this.len=e.tokens.length,this.eof=e.tokens[e.tokens.length-1],this.idx=0;}peek(e=0){let t=this.idx+e;return t>=this.len?this.eof:this.tokens[t]}advance(){let e=this.idx<this.len?this.tokens[this.idx]:this.eof;return e.kind!==\"eof\"&&(this.idx+=1),e}optional(e){let t=this.idx<this.len?this.tokens[this.idx]:this.eof;return t.kind===e?(t.kind!==\"eof\"&&(this.idx+=1),t):null}at(e){return (this.idx<this.len?this.tokens[this.idx]:this.eof).kind===e}at2(e,t){let o=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return o===e||o===t}at3(e,t,n){let r=(this.idx<this.len?this.tokens[this.idx]:this.eof).kind;return r===e||r===t||r===n}currentSpan(){return (this.idx<this.len?this.tokens[this.idx]:this.eof).span}position(){return this.idx}setPosition(e){this.idx=e;}isAtEnd(){return (this.idx<this.len?this.tokens[this.idx]:this.eof).kind===\"eof\"}},Ar=/^(PEPTIDE|RNA|DNA|CHEM|BLOB|G)([0-9]+)$/;function bo(i){let e=Ar.exec(i);if(e===null)return null;let t=e[1],n=parseInt(e[2],10);switch(t){case \"PEPTIDE\":return {rawTypeName:\"PEPTIDE\",polymerType:x.PEPTIDE,number:n,isDnaShim:false,isGroup:false};case \"RNA\":return {rawTypeName:\"RNA\",polymerType:x.RNA,number:n,isDnaShim:false,isGroup:false};case \"DNA\":return {rawTypeName:\"DNA\",polymerType:x.RNA,number:n,isDnaShim:true,isGroup:false};case \"CHEM\":return {rawTypeName:\"CHEM\",polymerType:x.CHEM,number:n,isDnaShim:false,isGroup:false};case \"BLOB\":return {rawTypeName:\"BLOB\",polymerType:x.BLOB,number:n,isDnaShim:false,isGroup:false};case \"G\":return {rawTypeName:\"G\",polymerType:x.PEPTIDE,number:n,isDnaShim:false,isGroup:true};default:return null}}var yn=class{constructor(e,t,n){this.diagnostics=[];this.chains=[];this.chainById=new Map;this.pendingBonds=[];this.groups=[];this.atomIds=new ve;this.bondIds=new ve;this.cursor=new bn(e),this.source=e.source,this.lib=t,this.mode=n,this.annotations={perPolymer:new Map,version:\"\"};}parseDocument(){if(this.cursor.isAtEnd())return this.emit(\"warning\",\"empty-helm\",\"Empty HELM string\"),{mol:me(),diagnostics:this.diagnostics};if(this.parseSimplePolymers(),this.expectDollarSeparator(1),this.parseConnections(),this.expectDollarSeparator(2),this.parseGroupsSection(),this.expectDollarSeparator(3),this.parseAnnotationsSection(),this.cursor.at(\"dollar\")&&(this.cursor.advance(),this.parseVersionTrailer()),!this.cursor.isAtEnd())for(this.emit(\"warning\",\"extra-section-separator\",\"Unexpected trailing tokens after HELM document\",this.cursor.currentSpan());!this.cursor.isAtEnd();)this.cursor.advance();return {mol:this.finalize(),diagnostics:this.diagnostics}}expectDollarSeparator(e){if(this.cursor.at(\"dollar\")){this.cursor.advance();return}this.emit(\"error\",\"missing-section-separator\",`Expected '$' separator before section ${e+1}`,this.cursor.currentSpan());}parseSimplePolymers(){if(!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()))for(this.parsePolymer();this.cursor.at(\"pipe\");){if(this.cursor.advance(),this.cursor.at(\"dollar\")||this.cursor.isAtEnd()){this.emit(\"warning\",\"empty-polymer-body\",\"Empty polymer after '|'\",this.cursor.currentSpan());return}this.parsePolymer();}}parsePolymer(){let e=this.cursor.currentSpan(),t=this.cursor.optional(\"identifier\");if(t===null){this.emit(\"error\",\"unexpected-token\",`Expected polymer id, got '${this.cursor.peek().value}'`,this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let n=bo(t.value);if(n===null){this.emit(\"error\",\"unknown-polymer-type\",`Unknown polymer type '${t.value}'`,t.span),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.chainById.has(t.value)&&this.emit(\"warning\",\"duplicate-polymer-id\",`Duplicate polymer id '${t.value}'`,t.span),this.cursor.optional(\"lbrace\")===null){this.emit(\"error\",\"unexpected-token\",`Expected '{' after polymer id '${t.value}'`,this.cursor.currentSpan());return}let o={id:t.value,polymerType:n.polymerType,rawTypeName:n.rawTypeName,rawNumber:n.number,backboneAtoms:[],allAtoms:[],bonds:[],span:{start:e.start,end:e.end}};if(this.chains.push(o),this.chainById.set(o.id,o),this.cursor.at(\"rbrace\"))this.emit(\"warning\",\"empty-polymer-body\",`Empty body for polymer '${o.id}'`,this.cursor.currentSpan());else if(n.isGroup)this.parseGroupBody(o);else switch(n.polymerType){case x.PEPTIDE:this.parsePeptideBody(o);break;case x.RNA:this.parseRnaBody(o,n.isDnaShim),n.isDnaShim&&this.emit(\"info\",\"dna-emitted-as-rna\",`DNA polymer '${o.id}' will be emitted as RNA on canonicalize`,t.span);break;case x.CHEM:this.parseChemBody(o);break;case x.BLOB:this.parseBlobBody(o);break;}if(this.cursor.optional(\"rbrace\")===null){this.emit(\"error\",\"unterminated-brace\",`Expected '}' to close polymer '${o.id}'`,this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let r=this.cursor.optional(\"quote-string\");r!==null&&(o.annotation=r.value);}parsePeptideBody(e){for(this.parsePeptideItem(e);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rbrace\")||this.cursor.at(\"gt\")));)this.parsePeptideItem(e);if(this.cursor.at(\"gt\")){let t=this.cursor.currentSpan();this.cursor.advance(),this.emit(\"warning\",\"peptide-cyclic-without-closure\",`Peptide '${e.id}' marked cyclic with '>' \\u2014 no explicit closure connection emitted`,t);}}parsePeptideItem(e){if(this.cursor.at(\"lparen\"))this.parsePeptideAlternation(e);else {let t=this.parsePeptideAtom(e);this.maybeRepeatBracket(e,[t]);}this.maybeAttachAnnotation(e);}parsePeptideAtom(e){let t=this.consumeMonomerSymbol(false),{symbol:n,annotation:o,ambiguity:r,ambiguityKind:s,isInlineSmiles:a,rawPayload:d,inlineSource:l,span:u}=t,c=this.makeAtom(e,g.AA,n);o!==void 0&&(c.tag=o),r!==void 0&&(c.bio.ambiguity=r),s!==void 0&&(c.bio.ambiguityKind=s),l!==void 0&&(c.inlineSource=l),a&&this.registerInlineSmiles(d,u,x.PEPTIDE),this.addToChain(e,c,true);let m=e.backboneAtoms[e.backboneAtoms.length-2];return m!==void 0&&this.addBond(e,m,c,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),c}parsePeptideAlternation(e){let t=this.cursor.currentSpan();if(this.cursor.advance(),this.peptideContentIsSubsequence()){let l=e.backboneAtoms.length;for(this.parsePeptideItem(e);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rparen\")||this.cursor.isAtEnd()));)this.parsePeptideItem(e);this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' to close repeat sub-sequence\",this.cursor.currentSpan());let u=e.backboneAtoms.slice(l);this.maybeRepeatBracket(e,u),this.maybeAttachAnnotation(e);return}let n=[],o=null;for(;!this.cursor.at(\"rparen\")&&!this.cursor.isAtEnd();){let l=this.parseAlternationCandidate(x.PEPTIDE);if(n.push(l),this.cursor.at(\"comma\"))o===\"and\"&&this.emit(\"warning\",\"mixed-separator-in-alternation\",\"Mixed ',' and '+' separators in alternation\",this.cursor.currentSpan()),o=\"or\",this.cursor.advance();else if(this.cursor.at(\"plus\"))o===\"or\"&&this.emit(\"warning\",\"mixed-separator-in-alternation\",\"Mixed ',' and '+' separators in alternation\",this.cursor.currentSpan()),o=\"and\",this.cursor.advance();else break}this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' to close alternation\",this.cursor.currentSpan());let r=o===\"and\"?\"+\":\",\",s=`(${n.map(l=>l.symbol+(l.ratio!==void 0?`:${String(l.ratio)}`:\"\")).join(r)})`,a=this.makeAtom(e,g.AA,\"?\");a.bio.ambiguity=s,a.bio.ambiguityKind=o===\"and\"?\"and\":\"or\",this.addToChain(e,a,true);let d=e.backboneAtoms[e.backboneAtoms.length-2];if(d!==void 0&&this.addBond(e,d,a,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),o===\"and\")for(let l of n)typeof l.ratio==\"number\"&&l.ratio<0&&this.emit(\"error\",\"ratio-and-negative\",`Negative ratio ${l.ratio} in AND mixture`,t);this.maybeRepeatBracket(e,[a]),this.maybeAttachAnnotation(e);}peptideContentIsSubsequence(){let e=1,t=0;for(;;){let n=this.cursor.peek(t);if(n.kind===\"eof\")return  false;if(n.kind===\"lparen\"){e+=1,t+=1;continue}if(n.kind===\"rparen\"){if(e-=1,e===0)return  true;t+=1;continue}if(e===1){if(n.kind===\"dot\")return  true;if(n.kind===\"comma\"||n.kind===\"plus\"||n.kind===\"colon\")return  false}if(t+=1,t>1024)return  false}}parseAlternationCandidate(e){let{symbol:t,isInlineSmiles:n,rawPayload:o,span:r}=this.consumeMonomerSymbol(true);n&&this.registerInlineSmiles(o,r,e);let s;if(this.cursor.optional(\"colon\")!==null){let a=this.cursor.peek();a.kind===\"integer\"||a.kind===\"decimal\"?(this.cursor.advance(),s=parseFloat(a.value)):a.kind===\"question\"?(this.cursor.advance(),s=\"?\"):this.emit(\"error\",\"unexpected-token\",\"Expected ratio after ':' in alternation\",a.span);}return s===void 0?{symbol:t}:{symbol:t,ratio:s}}parseRnaBody(e,t){for(this.parseRnaItem(e,t);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rbrace\")||this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseRnaItem(e,t);}parseRnaItem(e,t){if(this.cursor.at(\"lparen\")){this.parseRnaAlternation(e,t);return}if(this.cursor.at(\"asterisk\")){this.cursor.currentSpan();this.cursor.advance();let l=this.makeAtom(e,g.NUCLEOTIDE,\"*\");this.addToChain(e,l,true);let u=e.backboneAtoms[e.backboneAtoms.length-2];u!==void 0&&this.addBond(e,u,l,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),this.maybeRepeatBracket(e,[l]),this.maybeAttachAnnotation(e);return}let n=this.parseRnaSugar(e,t);this.maybeAttachAnnotation(e);let o;this.cursor.at(\"lparen\")&&(this.cursor.advance(),this.cursor.at(\"rparen\")||(o=this.parseRnaBaseSymbol(e),this.maybeAttachAnnotationTo(o)),this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' after RNA base\",this.cursor.currentSpan()),o!==void 0&&(this.addBond(e,n,o,\"branch\",{kind:\"numeric\",r:3},{kind:\"numeric\",r:1}),n.branchAtom=o));let r;this.canStartRnaLinker()&&(r=this.parseRnaLinker(e),this.maybeAttachAnnotationTo(r)),r!==void 0&&this.addBond(e,n,r,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1});let s=e.backboneAtoms.indexOf(n);if(s>0){let d=e.backboneAtoms[s-1];this.addBond(e,d,n,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1});}let a=[n];o!==void 0&&a.push(o),r!==void 0&&a.push(r),this.maybeRepeatBracket(e,a);}canStartRnaLinker(){let e=this.cursor.peek().kind;return e===\"identifier\"||e===\"inline-smiles\"||e===\"asterisk\"}parseRnaSugar(e,t){let{symbol:n,isInlineSmiles:o,rawPayload:r,inlineSource:s,span:a}=this.consumeMonomerSymbol(false),d=this.makeAtom(e,g.SUGAR,n);return s!==void 0&&(d.inlineSource=s),o&&this.registerInlineSmiles(r,a,x.RNA),this.addToChain(e,d,true),d}parseRnaBaseSymbol(e){let{symbol:t,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(false),a=this.makeAtom(e,g.BASE,t);return r!==void 0&&(a.inlineSource=r),n&&this.registerInlineSmiles(o,s,x.RNA),this.addToChain(e,a,false),a}parseRnaLinker(e){if(this.cursor.at(\"asterisk\")){this.cursor.currentSpan();this.cursor.advance();let l=this.makeAtom(e,g.LINKER,\"*\");return this.addToChain(e,l,true),l}let{symbol:t,isInlineSmiles:n,rawPayload:o,inlineSource:r,span:s}=this.consumeMonomerSymbol(false),a=this.makeAtom(e,g.LINKER,t);return r!==void 0&&(a.inlineSource=r),n&&this.registerInlineSmiles(o,s,x.RNA),this.addToChain(e,a,true),a}parseRnaAlternation(e,t){let n=e.backboneAtoms.length;if(this.cursor.advance(),this.looksLikeFlatAlternation()){let r=[],s=null;for(;!this.cursor.at(\"rparen\")&&!this.cursor.isAtEnd();)if(r.push(this.parseAlternationCandidate(x.RNA)),this.cursor.at(\"comma\"))s=\"or\",this.cursor.advance();else if(this.cursor.at(\"plus\"))s=\"and\",this.cursor.advance();else break;this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' in RNA alternation\",this.cursor.currentSpan());let a=s===\"and\"?\"+\":\",\",d=`(${r.map(c=>c.symbol+(c.ratio!==void 0?`:${String(c.ratio)}`:\"\")).join(a)})`,l=this.makeAtom(e,g.BASE,\"?\");l.bio.ambiguity=d,l.bio.ambiguityKind=s===\"and\"?\"and\":\"or\",this.addToChain(e,l,true);let u=e.backboneAtoms[e.backboneAtoms.length-2];u!==void 0&&this.addBond(e,u,l,\"backbone\",{kind:\"numeric\",r:2},{kind:\"numeric\",r:1}),this.maybeRepeatBracket(e,[l]),this.maybeAttachAnnotation(e);return}for(this.parseRnaItem(e,t);this.cursor.at(\"dot\")&&(this.cursor.advance(),!(this.cursor.at(\"rparen\")||this.cursor.isAtEnd()));)this.parseRnaItem(e,t);this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' in RNA repeat\",this.cursor.currentSpan());let o=e.backboneAtoms.slice(n);this.maybeRepeatBracket(e,o),this.maybeAttachAnnotation(e);}looksLikeFlatAlternation(){let e=1,t=0,n=false;for(;;){let o=this.cursor.peek(t);if(o.kind===\"eof\")return n;if(o.kind===\"rparen\"){if(e-=1,e===0)return n}else {if(o.kind===\"lparen\")return  false;if(o.kind===\"dot\")return  false;e===1&&(o.kind===\"comma\"||o.kind===\"plus\")&&(n=true);}if(t+=1,t>256)return n}}parseChemBody(e){let t;if(this.cursor.at(\"asterisk\"))this.cursor.advance(),t=this.makeAtom(e,g.CHEM,\"*\"),this.addToChain(e,t,true);else {let{symbol:n,isInlineSmiles:o,rawPayload:r,inlineSource:s,span:a}=this.consumeMonomerSymbol(false);t=this.makeAtom(e,g.CHEM,n),s!==void 0&&(t.inlineSource=s),o&&this.registerInlineSmiles(r,a,x.CHEM),this.addToChain(e,t,true);}this.maybeAttachAnnotation(e),this.cursor.at(\"apos\")&&this.maybeRepeatBracket(e,[t]),this.cursor.at(\"rbrace\")||(this.emit(\"error\",\"chem-multiple-monomers\",`CHEM polymer '${e.id}' must contain exactly one monomer`,this.cursor.currentSpan()),this.skipUntil([\"rbrace\",\"eof\"]));}parseBlobBody(e){let t,n,o=false,r=\"\",s,a=this.cursor.currentSpan();if(this.cursor.at(\"inline-smiles\")){let l=this.cursor.advance();o=Be(l.value),r=l.value,t=l.value,n=l.value,s=l.value,a=l.span;}else if(this.cursor.at(\"identifier\")){let l=this.cursor.advance();t=l.value,n=l.value,a=l.span;}else this.emit(\"error\",\"unknown-blobtype\",\"Expected BLOB identifier\",this.cursor.currentSpan()),t=\"?\",n=\"?\";let d=this.makeAtom(e,g.BLOB,t);d.bio.blobtype=n,s!==void 0&&(d.inlineSource=s),o&&this.registerInlineSmiles(r,a,x.BLOB),this.addToChain(e,d,true),this.maybeAttachAnnotation(e);}parseGroupBody(e){let t=0;for(;;){let n=this.cursor.peek();if(n.kind===\"eof\"||t===0&&n.kind===\"rbrace\")break;n.kind===\"lbrace\"&&(t+=1),n.kind===\"rbrace\"&&(t-=1),this.cursor.advance();}}parseConnections(){if(!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()))for(this.parseConnection();this.cursor.at(\"pipe\")&&(this.cursor.advance(),!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseConnection();}parseConnection(){let e=this.cursor.currentSpan(),t=this.cursor.optional(\"identifier\");if(t===null){this.emit(\"error\",\"unexpected-token\",\"Expected chain id in connection\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.cursor.optional(\"comma\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ',' in connection\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let n=this.cursor.optional(\"identifier\");if(n===null){this.emit(\"error\",\"unexpected-token\",\"Expected second chain id in connection\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.cursor.optional(\"comma\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ',' before connection position\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let o=this.parsePosition();if(this.cursor.optional(\"colon\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ':' between position and R-group\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let r=this.parseRGroupSpec();if(this.cursor.optional(\"dash\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected '-' between connection endpoints\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let s=this.parsePosition();if(this.cursor.optional(\"colon\")===null){this.emit(\"error\",\"unexpected-token\",\"Expected ':' before second R-group\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let a=this.parseRGroupSpec(),d=this.cursor.optional(\"quote-string\"),l=r.kind===\"pair\"&&a.kind===\"pair\"?\"hbond\":\"cross-polymer\",u={chain1:t.value,pos1:o,r1:r,chain2:n.value,pos2:s,r2:a,kind:l,span:{start:e.start,end:d?.span.end??this.cursor.peek().span.start},...d!==null?{tag:d.value}:{}};this.pendingBonds.push(u);}parsePosition(){let e=this.cursor.peek();return e.kind===\"integer\"?(this.cursor.advance(),{kind:\"index\",value:parseInt(e.value,10)}):e.kind===\"question\"?(this.cursor.advance(),{kind:\"any\"}):e.kind===\"identifier\"?(this.cursor.advance(),this.emit(\"info\",\"symbol-position-reference\",`Connection position uses monomer symbol '${e.value}' as chain-level ambiguity`,e.span),{kind:\"symbol\",value:e.value}):(this.emit(\"error\",\"invalid-position\",`Expected position (integer, '?', or symbol), got '${e.value}'`,e.span),{kind:\"any\"})}parseRGroupSpec(){let e=this.cursor.peek();if(e.kind===\"question\")return this.cursor.advance(),{kind:\"unspecified\"};if(e.kind===\"asterisk\")return this.cursor.advance(),{kind:\"wildcard\"};if(e.kind===\"identifier\"){if(this.cursor.advance(),e.value===\"pair\")return {kind:\"pair\"};let t=/^R([1-9][0-9]*)$/.exec(e.value);return t===null?(this.emit(\"error\",\"invalid-rgroup\",`Expected R-group label, got '${e.value}'`,e.span),{kind:\"unspecified\"}):{kind:\"numeric\",r:parseInt(t[1],10)}}return this.emit(\"error\",\"invalid-rgroup\",`Expected R-group label, got '${e.value}'`,e.span),{kind:\"unspecified\"}}parseGroupsSection(){if(!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()))for(this.parseGroupOrBondRatio();this.cursor.at(\"pipe\")&&(this.cursor.advance(),!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseGroupOrBondRatio();}parseGroupOrBondRatio(){let e=this.cursor.optional(\"identifier\");if(e===null){this.emit(\"error\",\"unexpected-token\",\"Expected group or bond-ratio identifier\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}this.cursor.at(\"lparen\")?this.parseGroupAfterId(e):this.cursor.at(\"plus\")?this.parseBondRatioAfterId(e):(this.emit(\"warning\",\"unexpected-token\",`Expected '(' or '+' after id '${e.value}' in section 3`,this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]));}parseGroupAfterId(e){let t=bo(e.value);(t===null||!t.isGroup)&&this.emit(\"error\",\"unknown-group-reference\",`Group id must be 'G<n>', got '${e.value}'`,e.span),this.cursor.advance();let n=[],o=\"or\",r=null;for(;!this.cursor.at(\"rparen\")&&!this.cursor.isAtEnd();){let s=this.parseGroupMember();if(s!==null&&n.push(s),this.cursor.at(\"comma\"))r===null&&(r=\"or\",o=\"or\"),this.cursor.advance();else if(this.cursor.at(\"plus\"))r===null&&(r=\"and\",o=\"and\"),this.cursor.advance();else break}this.cursor.optional(\"rparen\")===null&&this.emit(\"error\",\"unterminated-paren\",\"Expected ')' to close group\",this.cursor.currentSpan()),this.groups.push({id:e.value,kind:o,members:n});}parseGroupMember(){let e=this.cursor.optional(\"identifier\");if(e===null)return this.emit(\"error\",\"unexpected-token\",\"Expected group member id\",this.cursor.currentSpan()),null;let t;return this.cursor.optional(\"colon\")!==null&&(t=this.parseRatio()),t===void 0?{target:e.value}:{target:e.value,ratio:t}}parseRatio(){let e=this.cursor.peek();if(e.kind===\"integer\"||e.kind===\"decimal\"){this.cursor.advance();let t=parseFloat(e.value);if(this.cursor.at(\"dash\")){this.cursor.peek();if(this.cursor.peek(1).kind===\"integer\"){this.cursor.advance();let o=this.cursor.advance();this.emit(\"info\",\"ratio-range\",`Ratio range ${e.value}-${o.value}; using lower bound`,{start:e.span.start,end:o.span.end});}}return t}return e.kind===\"question\"?(this.cursor.advance(),\"?\"):(this.emit(\"error\",\"unexpected-token\",`Expected ratio after ':', got '${e.value}'`,e.span),0)}parseBondRatioAfterId(e){this.cursor.advance();let t=this.cursor.optional(\"identifier\");if(t===null){this.emit(\"error\",\"unexpected-token\",\"Expected second chain id in bond-ratio\",this.cursor.currentSpan());return}let n;if(this.cursor.optional(\"colon\")!==null){let r=this.parseRatio();typeof r==\"number\"&&(n=r);}let o=this.pendingBonds.find(r=>r.chain1===e.value&&r.chain2===t.value||r.chain1===t.value&&r.chain2===e.value);if(o===void 0){this.emit(\"warning\",\"bond-ratio-no-matching-bond\",`Bond-ratio for ${e.value}+${t.value} has no matching cross-polymer bond`,e.span);return}n!==void 0&&(o.ratio={numerator:n});}parseAnnotationsSection(){if(this.cursor.at(\"dollar\")||this.cursor.isAtEnd())return;this.cursor.position();if(this.cursor.at(\"lbrace\")){this.parseAnnotation20(),this.cursor.at(\"pipe\")&&(this.emit(\"info\",\"annotation-mixed-versions\",\"Mixed HELM 2.0 JSON and HELM 1.0 pipe annotations\",this.cursor.currentSpan()),this.cursor.advance(),this.parseAnnotation10Entries());return}this.parseAnnotation10Entries();}parseAnnotation20(){let e=this.cursor.currentSpan(),t=0,n=e.end;for(;!this.cursor.isAtEnd();){let s=this.cursor.peek();if(s.kind===\"lbrace\")t+=1;else if(s.kind===\"rbrace\"&&(t-=1,t===0)){n=s.span.end,this.cursor.advance();break}this.cursor.advance();}let o=this.source.slice(e.start,n),r=null;try{r=JSON.parse(o);}catch{this.emit(\"warning\",\"annotation-malformed-json\",\"Annotation block is not valid JSON\",{start:e.start,end:n}),this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:o};return}if(r!==null&&typeof r==\"object\"&&!Array.isArray(r)){let s=new Map(this.annotations.perPolymer);for(let[a,d]of Object.entries(r))d!==null&&typeof d==\"object\"&&!Array.isArray(d)?(s.set(a,{...d}),this.chainById.has(a)||this.emit(\"warning\",\"annotation-unknown-polymer\",`Annotation references unknown polymer '${a}'`,e)):s.set(a,{value:d});this.annotations={perPolymer:s,version:this.annotations.version};}else this.emit(\"warning\",\"annotation-malformed-json\",\"Annotation block parsed but is not an object\",{start:e.start,end:n}),this.annotations={perPolymer:this.annotations.perPolymer,version:this.annotations.version,raw:o};}parseAnnotation10Entries(){for(this.parseAnnotation10One();this.cursor.at(\"pipe\")&&(this.cursor.advance(),!(this.cursor.at(\"dollar\")||this.cursor.isAtEnd()));)this.parseAnnotation10One();}parseAnnotation10One(){let e=this.cursor.optional(\"identifier\");if(e===null){this.emit(\"warning\",\"annotation-malformed-json\",\"Expected polymer-id in HELM 1.0 annotation\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}if(this.cursor.optional(\"lbrace\")===null){this.emit(\"warning\",\"annotation-malformed-json\",\"Expected '{' after polymer-id\",this.cursor.currentSpan()),this.skipUntil([\"pipe\",\"dollar\",\"eof\"]);return}let t=[];for(;!this.cursor.at(\"rbrace\")&&!this.cursor.isAtEnd();)t.push(this.cursor.advance().value);if(this.cursor.optional(\"rbrace\")===null){this.emit(\"error\",\"unterminated-brace\",\"Expected '}' to close annotation\",this.cursor.currentSpan());return}let n=t.join(\"\").trim(),o=new Map(this.annotations.perPolymer),r=o.get(e.value)??{};n===\"ss\"||n===\"as\"?o.set(e.value,{...r,strandtype:n}):o.set(e.value,{...r,[n]:true}),this.chainById.has(e.value)||this.emit(\"warning\",\"annotation-unknown-polymer\",`Annotation references unknown polymer '${e.value}'`,e.span),this.annotations={perPolymer:o,version:this.annotations.version};}parseVersionTrailer(){let e=this.cursor.optional(\"identifier\");if(e===null){this.annotations={...this.annotations,version:\"\"};return}let t=e.value;if(this.cursor.at(\"dot\")&&this.cursor.peek(1).kind===\"integer\"){this.cursor.advance();let n=this.cursor.advance();t=`${e.value}.${n.value}`;}this.annotations={...this.annotations,version:t};}skipUntil(e){for(;!this.cursor.isAtEnd();){if(e.includes(this.cursor.peek().kind))return;this.cursor.advance();}}consumeMonomerSymbol(e){let t=this.cursor.peek();if(t.kind===\"inline-smiles\"){this.cursor.advance();let n=Be(t.value);return {symbol:t.value,isInlineSmiles:n,rawPayload:t.value,inlineSource:t.value,span:t.span}}if(t.kind===\"identifier\"){this.cursor.advance();let n=t.value,o=t.span;for(;this.cursor.peek().kind===\"dash\"&&this.cursor.peek(1).kind===\"integer\"&&(this.cursor.peek(2).kind===\"identifier\"||this.cursor.peek(2).kind===\"dash\");){this.cursor.advance();let s=this.cursor.advance();if(n=`${n}-${s.value}`,o=s.span,this.cursor.peek().kind===\"identifier\"){let a=this.cursor.advance();n=`${n}${a.value}`,o=a.span;}}return {symbol:n,isInlineSmiles:false,rawPayload:n,span:{start:t.span.start,end:o.end}}}if(t.kind===\"asterisk\"||t.kind===\"underscore\"||t.kind===\"question\")return this.cursor.advance(),{symbol:t.value,isInlineSmiles:false,rawPayload:t.value,span:t.span};if(t.kind===\"integer\"&&this.cursor.peek(1).kind===\"identifier\"){let n=this.cursor.advance(),o=this.cursor.advance(),r=`${n.value}${o.value}`;return {symbol:r,isInlineSmiles:false,rawPayload:r,span:{start:n.span.start,end:o.span.end}}}return this.emit(\"error\",\"unexpected-token\",`Expected monomer symbol, got '${t.value}'`,t.span),{symbol:\"?\",isInlineSmiles:false,rawPayload:\"\",span:t.span}}maybeRepeatBracket(e,t){if(!this.cursor.at(\"apos\"))return;let n=this.cursor.currentSpan();this.cursor.advance();let o=this.cursor.optional(\"integer\");if(o===null){this.emit(\"error\",\"unexpected-token\",\"Expected integer in repeat bracket\",this.cursor.currentSpan()),this.cursor.optional(\"apos\");return}let r=parseInt(o.value,10),s=r;if(this.cursor.at(\"dash\")){this.cursor.advance();let a=this.cursor.optional(\"integer\");a===null?this.emit(\"error\",\"unexpected-token\",\"Expected integer after '-' in repeat bracket\",this.cursor.currentSpan()):s=parseInt(a.value,10);}if(this.cursor.optional(\"apos\")===null&&this.emit(\"error\",\"unterminated-apostrophe\",\"Expected closing apostrophe\",this.cursor.currentSpan()),t.length===0){this.emit(\"warning\",\"repeat-on-empty-bracket\",\"Repeat bracket applied to empty content\",n);return}if(s<r){this.emit(\"warning\",\"repeat-range-inverted\",`Repeat range ${r}-${s} has max < min; swapping`,n);let a=r;r=s,s=a;}if(r===0&&s===0){this.emit(\"warning\",\"repeat-zero-count\",\"Repeat bracket with zero count\",n);return}s>1e4&&this.emit(\"warning\",\"bracket-repeat-too-large\",`Repeat range upper bound ${s} > 10000`,n),e.polymerType===x.CHEM&&this.emit(\"error\",\"repeat-on-non-iterable-polymer\",`Repeat bracket not allowed on CHEM polymer '${e.id}'`,n),this.groups.push({id:`${e.id}/bracket@${t[0]?.id??0}`,kind:\"bracket\",members:t.map(a=>({target:String(a.id)})),repeat:{min:r,max:s}});}maybeAttachAnnotation(e){let t=e.backboneAtoms[e.backboneAtoms.length-1];t!==void 0&&this.maybeAttachAnnotationTo(t);}maybeAttachAnnotationTo(e){if(e===void 0)return;let t=this.cursor.optional(\"quote-string\");t!==null&&(e.tag=t.value);}registerInlineSmiles(e,t,n){if(Be(e)){if(this.lib===null){this.emit(\"info\",\"inline-smiles-no-lib\",\"Inline SMILES seen but no monomer library available for registration\",t);return}try{this.lib.addMonomer;let o=this.lib.registerInlineSmilesMonomer;typeof o==\"function\"&&o.call(this.lib,n,e);}catch(o){let r=o instanceof Error?o.message:String(o);this.emit(\"warning\",\"inline-smiles-without-r-groups\",`Inline SMILES registration failed: ${r}`,t);}}}makeAtom(e,t,n){return {id:this.atomIds.next(),p:{x:0,y:0},biotype:t,symbol:n,monomer:null,bio:{chainId:e.id,positionInChain:0,continuousId:0},hidden:false,selected:false,highlighted:false}}addToChain(e,t,n){e.allAtoms.push(t),n&&(e.backboneAtoms.push(t),t.bio.positionInChain=e.backboneAtoms.length);}addBond(e,t,n,o,r,s){let a=this.bondIds.next();e.bonds.push({id:a,a1:t,a2:n,kind:o,r1:r,r2:s});}finalize(){let e=[];for(let a of this.pendingBonds){let d=this.chainById.get(a.chain1),l=this.chainById.get(a.chain2);if(d===void 0){this.emit(\"error\",\"unknown-chain-reference\",`Connection references unknown chain '${a.chain1}'`,a.span);continue}if(l===void 0){this.emit(\"error\",\"unknown-chain-reference\",`Connection references unknown chain '${a.chain2}'`,a.span);continue}let u=this.resolveAtomByPosition(d,a.pos1,a.span),c=this.resolveAtomByPosition(l,a.pos2,a.span);if(u===null||c===null)continue;a.r1.kind===\"pair\"&&u.branchAtom!==void 0&&(u=u.branchAtom),a.r2.kind===\"pair\"&&c.branchAtom!==void 0&&(c=c.branchAtom);let p={id:this.bondIds.next(),a1:u,a2:c,kind:a.kind,r1:a.r1,r2:a.r2,...a.tag!==void 0?{tag:a.tag}:{},...a.ratio!==void 0?{ratio:a.ratio}:{}};e.push(p);}let t=[],n=[],o=[];for(let a of this.chains){for(let c of a.allAtoms)t.push(c);for(let c of a.bonds)n.push(c);let d=this.annotations.perPolymer.get(a.id),l=d===void 0?void 0:d.strandtype,u=l===\"ss\"||l===\"as\"?l:void 0;o.push({id:a.id,polymerType:a.polymerType,backboneAtoms:a.backboneAtoms,bonds:a.bonds,...a.annotation!==void 0?{annotation:a.annotation}:{},...u!==void 0?{strandType:u}:{}});}for(let a of e)n.push(a);let r=0;for(let a of this.chains)for(let d of a.backboneAtoms)r+=1,d.bio.continuousId=r,d.branchAtom!==void 0&&(r+=1,d.branchAtom.bio.continuousId=r);let s=[];for(let a of this.groups)s.push({id:a.id,kind:a.kind,members:a.members,...a.repeat!==void 0?{repeat:a.repeat}:{}});return {atoms:t,bonds:n,chains:o,groups:s,annotations:this.annotations}}sourceOrderAtoms(e){let t=[];for(let n of e.backboneAtoms)t.push(n),n.branchAtom!==void 0&&t.push(n.branchAtom);return t}resolveAtomByPosition(e,t,n){if(t.kind===\"any\")return e.backboneAtoms[0]??null;if(t.kind===\"symbol\"){let s=e.backboneAtoms.find(a=>a.symbol===t.value);if(s===void 0){let a=e.allAtoms.find(d=>d.symbol===t.value);return a===void 0?(this.emit(\"warning\",\"position-out-of-range\",`Chain '${e.id}' has no monomer with symbol '${t.value}'`,n),e.backboneAtoms[0]??null):a}return s}let o=this.sourceOrderAtoms(e),r=t.value;return r<1||r>o.length?(this.emit(\"error\",\"position-out-of-range\",`Position ${r} out of range for chain '${e.id}' (length ${o.length})`,n),e.backboneAtoms[0]??null):o[r-1]}emit(e,t,n,o){let r={severity:e,code:t,message:n,...o!==void 0?{span:{start:o.start,end:o.end}}:{}};if(this.diagnostics.push(r),this.mode===\"strict\"&&e===\"error\")throw new F(t,n,{...o!==void 0?{span:{start:o.start,end:o.end}}:{}})}};function Mr(i,e,t){for(let n of t){if(n.kind!==\"backbone\"||n.r1.kind!==\"numeric\"||n.r2.kind!==\"numeric\")continue;let o=n.a1.id===i.id&&n.a2.id===e.id&&n.r1.r===2&&n.r2.r===1,r=n.a1.id===e.id&&n.a2.id===i.id&&n.r1.r===2&&n.r2.r===1;if(o||r)return  true}return  false}function Tr(i){let e=(c,m)=>c.polymerType===x.CHEM||c.polymerType===x.BLOB?true:!Mr(c.backboneAtoms[m],c.backboneAtoms[m+1],i.bonds),t=false;for(let c of i.chains){for(let m=0;m<c.backboneAtoms.length-1;m++)if(e(c,m)){t=true;break}if(t)break}if(!t)return i;let n=new Set(i.chains.map(c=>c.id)),o=c=>{let m=1;for(;n.has(`${c}${m}`);)m+=1;let p=`${c}${m}`;return n.add(p),p},r=[];for(let c of i.chains){let m=[[]],p=m[0];for(let h=0;h<c.backboneAtoms.length;h++){let y=c.backboneAtoms[h];p.push(y),h<c.backboneAtoms.length-1&&e(c,h)&&(p=[],m.push(p));}for(let h=0;h<m.length;h++){let f={id:h===0?c.id:o(c.polymerType),polymerType:c.polymerType,atoms:m[h]};h===0&&c.annotation!==void 0&&(f.annotation=c.annotation),r.push(f);}}let s=new Map;for(let c of r)for(let m=0;m<c.atoms.length;m++){let p=c.atoms[m];s.set(p.id,{chainId:c.id,pos:m+1}),p.branchAtom!==void 0&&s.set(p.branchAtom.id,{chainId:c.id,pos:m+1});}let a=new Map;for(let c of i.atoms){let m=s.get(c.id);if(m===void 0){a.set(c.id,c);continue}if(c.bio.chainId===m.chainId&&c.bio.positionInChain===m.pos){a.set(c.id,c);continue}a.set(c.id,{...c,bio:{...c.bio,chainId:m.chainId,positionInChain:m.pos}});}for(let c of i.atoms){if(c.branchAtom===void 0)continue;let m=a.get(c.id),p=a.get(c.branchAtom.id);m===void 0||p===void 0||(m.branchAtom=p);}let d=i.bonds.map(c=>{let m=a.get(c.a1.id)??c.a1,p=a.get(c.a2.id)??c.a2;return m===c.a1&&p===c.a2?c:{...c,a1:m,a2:p}}),l=r.map(c=>{let m=c.atoms.map(f=>a.get(f.id)??f),p=new Set;for(let f of c.atoms)p.add(f.id),f.branchAtom!==void 0&&p.add(f.branchAtom.id);let h=[];for(let f of d)p.has(f.a1.id)&&p.has(f.a2.id)&&h.push(f);return {id:c.id,polymerType:c.polymerType,backboneAtoms:m,bonds:h,...c.annotation!==void 0?{annotation:c.annotation}:{}}});return {atoms:i.atoms.map(c=>a.get(c.id)??c),bonds:d,chains:l,groups:i.groups,annotations:i.annotations}}function Pe(i,e){let t=Tr(i);return new gn(t,e??{}).emit()}var gn=class{constructor(e,t){this.mol=e,this.options=t;}emit(){let t=this.orderedChains().map(a=>this.emitPolymer(a)).join(\"|\"),n=this.emitConnections(),o=this.emitGroupsAndBondRatios(),r=this.emitAnnotations(),s=this.versionTrailer();return `${t}$${n}$${o}$${r}${s}`}orderedChains(){if(this.options.canonicalize!==true)return this.mol.chains;let e=this.mol.chains.slice();return e.sort((t,n)=>t.polymerType!==n.polymerType?t.polymerType<n.polymerType?-1:1:t.id<n.id?-1:t.id>n.id?1:0),e}emitPolymer(e){let t=this.emitChainBody(e),n=e.annotation!==void 0?`\"${ne(e.annotation)}\"`:\"\";return `${e.id}{${t}}${n}`}emitChainBody(e){switch(e.polymerType){case \"PEPTIDE\":return this.emitPeptideBody(e);case \"RNA\":return this.emitRnaBody(e);case \"CHEM\":return this.emitChemBody(e);case \"BLOB\":return this.emitBlobBody(e);default:return \"\"}}emitPeptideBody(e){let t=this.bracketsForChain(e.id),n=[],o=0,r=0,s=null;for(;o<e.backboneAtoms.length;){let a=e.backboneAtoms[o],d=t.find(u=>u.startAtomId===a.id);d!==void 0&&s===null&&(n.push(\"(\"),s=d,r+=1),n.push(this.emitMonomerToken(a));let l=a.tag!==void 0?`\"${ne(a.tag)}\"`:\"\";n.push(l),s!==null&&s.endAtomId===a.id&&(n.push(`)${go(s.min,s.max)}`),s=null,r-=1),o+=1,o<e.backboneAtoms.length&&n.push(\".\");}return n.join(\"\")}emitRnaBody(e){let t=this.bracketsForChain(e.id),n=[],o=0,r=true,s=null,a=l=>{s!==null&&s.endAtomId===l&&(n.push(`)${go(s.min,s.max)}`),s=null);},d=l=>{let u=t.find(c=>c.startAtomId===l);u!==void 0&&s===null&&(n.push(\"(\"),s=u);};for(;o<e.backboneAtoms.length;){let l=e.backboneAtoms[o];if(r||n.push(\".\"),r=false,l.biotype===g.NUCLEOTIDE){d(l.id),n.push(this.emitMonomerToken(l)),l.tag!==void 0&&n.push(`\"${ne(l.tag)}\"`),a(l.id),o+=1;continue}if(l.biotype===g.SUGAR){d(l.id),n.push(this.emitMonomerToken(l)),l.tag!==void 0&&n.push(`\"${ne(l.tag)}\"`),l.branchAtom!==void 0&&(n.push(\"(\"),n.push(this.emitMonomerToken(l.branchAtom)),l.branchAtom.tag!==void 0&&n.push(`\"${ne(l.branchAtom.tag)}\"`),n.push(\")\"));let u=e.backboneAtoms[o+1];u!==void 0&&u.biotype===g.LINKER?(n.push(this.emitMonomerToken(u)),u.tag!==void 0&&n.push(`\"${ne(u.tag)}\"`),a(u.id),o+=2):(a(l.id),o+=1);continue}d(l.id),n.push(this.emitMonomerToken(l)),l.tag!==void 0&&n.push(`\"${ne(l.tag)}\"`),a(l.id),o+=1;}return n.join(\"\")}emitChemBody(e){let t=e.backboneAtoms[0];if(t===void 0)return \"\";let n=t.tag!==void 0?`\"${ne(t.tag)}\"`:\"\";return `${this.emitMonomerToken(t)}${n}`}emitBlobBody(e){let t=e.backboneAtoms[0];if(t===void 0)return \"\";let n=t.tag!==void 0?`\"${ne(t.tag)}\"`:\"\";return `${this.emitMonomerToken(t)}${n}`}emitMonomerToken(e){let t;return e.inlineSource!==void 0?t=`[${e.inlineSource}]`:e.bio.ambiguity!==void 0&&(e.symbol===\"?\"||e.bio.ambiguity.startsWith(\"(\"))?t=e.bio.ambiguity:t=e.symbol,this.options.includeHighlights===true&&e.selected?`<span style='background:#bbf;'>${t}</span>`:t}emitConnections(){let e=[];for(let t of this.crossPolymerBonds())e.push(this.emitConnection(t));return e.join(\"|\")}*crossPolymerBonds(){let e=new Map;for(let t of this.mol.chains){let n=new Map;for(let o=0;o<t.backboneAtoms.length;o++)n.set(t.backboneAtoms[o].id,o);e.set(t.id,n);}for(let t of this.mol.bonds){if(t.kind===\"backbone\"){if(t.a1.bio.chainId===t.a2.bio.chainId){let n=e.get(t.a1.bio.chainId);if(n!==void 0){let o=n.get(t.a1.id),r=n.get(t.a2.id);if(o!==void 0&&r!==void 0&&Math.abs(o-r)===1)continue}}yield t;continue}if(t.kind===\"branch\"){if(t.a1.branchAtom!==void 0&&t.a1.branchAtom.id===t.a2.id||t.a2.branchAtom!==void 0&&t.a2.branchAtom.id===t.a1.id)continue;yield t;continue}yield t;}}emitConnection(e){let t=_o(e.r1,e.kind),n=_o(e.r2,e.kind),o=e.tag!==void 0?`\"${ne(e.tag)}\"`:\"\",r=String(this.connectionPosition(e.a1)),s=String(this.connectionPosition(e.a2));return `${e.a1.bio.chainId},${e.a2.bio.chainId},${r}:${t}-${s}:${n}${o}`}connectionPosition(e){return le(e,this.mol.chains.find(t=>t.id===e.bio.chainId))}emitGroupsAndBondRatios(){let e=[];for(let t of this.mol.groups)t.kind!==\"bracket\"&&e.push(this.emitGroup(t));for(let t of this.mol.bonds){if(t.kind!==\"cross-polymer\"||t.ratio===void 0)continue;let n=t.ratio.denominator!==void 0?`${t.ratio.numerator}/${t.ratio.denominator}`:`${t.ratio.numerator}`;e.push(`${t.a1.bio.chainId}+${t.a2.bio.chainId}:${n}`);}return e.join(\"|\")}emitGroup(e){let t=e.kind===\"and\"?\"+\":\",\",n=e.members.map(o=>Sr(o)).join(t);return `${e.id}(${n})`}emitAnnotations(){let e=this.mol.annotations.perPolymer;if(e.size===0)return \"\";let t={};for(let[n,o]of e)t[n]=o;return JSON.stringify(t)}versionTrailer(){let e=this.options.version??\"V2.0\";if(e===\"none\")return \"\";if(e===\"preserve\"){let t=this.mol.annotations.version;return t===\"\"?\"\":`$${t}`}return `$${e}`}bracketsForChain(e){let t=[],n=new Map;for(let o of this.mol.atoms)n.set(o.id,o.bio.chainId);for(let o of this.mol.groups){if(o.kind!==\"bracket\")continue;let r=[];for(let d of o.members){let l=parseInt(d.target,10);Number.isFinite(l)&&r.push(l);}if(r.length===0)continue;let s=new Set;for(let d of r){let l=n.get(d);l!==void 0&&s.add(l);}if(!s.has(e)||s.size>1)continue;let a=o.repeat??{min:1,max:1};t.push({members:r,min:a.min,max:a.max,set:new Set(r),startAtomId:r[0],endAtomId:r[r.length-1]});}return t}};function ne(i){let e=\"\";for(let t=0;t<i.length;t++){let n=i.charCodeAt(t);if(n===34){e+='\\\\\"';continue}if(n===92){e+=\"\\\\\\\\\";continue}if(n===10){e+=\"\\\\n\";continue}if(n===13){e+=\"\\\\r\";continue}if(n===9){e+=\"\\\\t\";continue}e+=i.charAt(t);}return e}function go(i,e){return i===e?`'${i}'`:`'${i}-${e}'`}function _o(i,e){switch(i.kind){case \"numeric\":return `R${i.r}`;case \"unspecified\":return \"?\";case \"wildcard\":return \"*\";case \"pair\":return \"pair\";case \"positional\":return `${i.position}:R${i.r}`;default:return \"?\"}}function Sr(i){return i.ratio===void 0?i.target:`${i.target}:${i.ratio}`}function vn(i){return new _n(i).run()}var _n=class{constructor(e){this.chainIdMap=new Map;this.mol=e;}run(){let e=this.mol.chains.slice().sort((m,p)=>m.polymerType!==p.polymerType?m.polymerType<p.polymerType?-1:1:xo(m.id,p.id)),t={},n=[];for(let m of e){let p=Er(m.polymerType);t[p]=(t[p]??0)+1;let h=`${p}${t[p]}`;this.chainIdMap.set(m.id,h),n.push(m);}let o=new Map;for(let m of this.mol.atoms){let p=this.chainIdMap.get(m.bio.chainId)??m.bio.chainId;o.set(m.id,{...m,bio:{...m.bio,chainId:p}});}for(let m of this.mol.atoms){if(m.branchAtom===void 0)continue;let p=o.get(m.id),h=o.get(m.branchAtom.id);p!==void 0&&h!==void 0&&(p.branchAtom=h);}let r=this.mol.bonds.map(m=>({...m,a1:o.get(m.a1.id)??m.a1,a2:o.get(m.a2.id)??m.a2})),s=new Map;for(let m of r)s.set(m.id,m);let a=n.map(m=>{let p=this.chainIdMap.get(m.id)??m.id,h=[];for(let f of m.backboneAtoms){let _=o.get(f.id);_!==void 0&&h.push(_);}let y=[];for(let f of m.bonds){let _=s.get(f.id);_!==void 0&&y.push(_);}return {id:p,polymerType:m.polymerType,backboneAtoms:h,bonds:y,...m.annotation!==void 0&&m.annotation.length>0?{annotation:m.annotation}:{}}}),d=new Map;for(let m of a)d.set(m.id,m);r.sort((m,p)=>{let h=vo(m.kind),y=vo(p.kind);if(h&&!y)return 1;if(!h&&y)return  -1;if(!h&&!y)return m.id-p.id;let f=m.a1.bio.chainId,_=p.a1.bio.chainId;if(f!==_)return f<_?-1:1;let b=m.a2.bio.chainId,A=p.a2.bio.chainId;if(b!==A)return b<A?-1:1;let w=le(m.a1,d.get(m.a1.bio.chainId)),k=le(p.a1,d.get(p.a1.bio.chainId));if(w!==k)return w-k;let C=le(m.a2,d.get(m.a2.bio.chainId)),I=le(p.a2,d.get(p.a2.bio.chainId));return C-I});let l=this.renumberGroups(this.mol.groups),u=this.rekeyAnnotations(this.mol.annotations);return {atoms:this.mol.atoms.map(m=>o.get(m.id)),bonds:r,chains:a,groups:l,annotations:u}}renumberGroups(e){let t=[],n=[];for(let r of e)r.kind===\"bracket\"?t.push(this.rekeyBracket(r)):n.push(r);n.sort((r,s)=>xo(r.id,s.id));let o={G:0};return n.map(r=>{o.G+=1;let s=`G${o.G}`;return {...r,id:s,members:r.members.map(a=>this.rekeyMember(a))}}).concat(t)}rekeyBracket(e){return e}rekeyMember(e){let t=this.chainIdMap.get(e.target);return t===void 0?e:e.ratio===void 0?{target:t}:{target:t,ratio:e.ratio}}rekeyAnnotations(e){let t=new Map;for(let[n,o]of e.perPolymer){let r=this.chainIdMap.get(n)??n;Object.keys(o).length!==0&&t.set(r,o);}return {perPolymer:t,version:e.version}}};function Er(i){switch(i){case \"PEPTIDE\":return \"PEPTIDE\";case \"RNA\":return \"RNA\";case \"CHEM\":return \"CHEM\";case \"BLOB\":return \"BLOB\";default:return \"BLOB\"}}function vo(i){return i===\"cross-polymer\"||i===\"hbond\"}function xo(i,e){let t=/^([A-Z]+)([0-9]+)$/.exec(i),n=/^([A-Z]+)([0-9]+)$/.exec(e);return t===null||n===null?i<e?-1:i>e?1:0:t[1]!==n[1]?t[1]<n[1]?-1:1:parseInt(t[2],10)-parseInt(n[2],10)}function wo(i){let e=Le(i),t=new Map;for(let a of i.atoms){let d=e.get(a.id);if(d===void 0||d===a.bio.continuousId){t.set(a.id,a);continue}t.set(a.id,{...a,bio:{...a.bio,continuousId:d}});}for(let a of i.atoms){if(a.branchAtom===void 0)continue;let d=t.get(a.id),l=t.get(a.branchAtom.id);d===void 0||l===void 0||(d.branchAtom=l);}let n=i.bonds.map(a=>{let d=t.get(a.a1.id),l=t.get(a.a2.id);return d===void 0||l===void 0||d===a.a1&&l===a.a2?a:{...a,a1:d,a2:l}}),o=new Map;for(let a of n)o.set(a.id,a);let r=i.chains.map(a=>{let d=[];for(let u of a.backboneAtoms){let c=t.get(u.id);d.push(c??u);}let l=[];for(let u of a.bonds){let c=o.get(u.id);l.push(c??u);}return {id:a.id,polymerType:a.polymerType,backboneAtoms:d,bonds:l,...a.annotation!==void 0?{annotation:a.annotation}:{}}});return {atoms:i.atoms.map(a=>t.get(a.id)??a),bonds:n,chains:r,groups:i.groups,annotations:i.annotations}}function xn(i,e){let n=ot(i,e??null,{mode:\"lenient\",resolveMonomers:false}),o=Cr(n.mol),r=wo(o.mol),s=new Map;for(let l of r.atoms)s.set(l.id,l.bio.continuousId);let a=new Map;for(let[l,u]of o.survivorByOldContinuousId){let c=s.get(u);c!==void 0&&a.set(l,c);}let d=Pe(r,{version:\"V2.0\"});return {srcHelm:i,resHelm:d,monomerMap:a}}function Cr(i){let e=new Map;for(let c of i.atoms)e.set(c.bio.continuousId,c.id);let t=new Set;for(let c of i.atoms)c.symbol===\"*\"&&t.add(c.id);if(t.size===0)return {mol:i,survivorByOldContinuousId:e};let n=new Map;for(let c of i.atoms)n.set(c.id,[]);for(let c of i.bonds)n.get(c.a1.id)?.push(c),n.get(c.a2.id)?.push(c);for(let c of t){let m=n.get(c)??[];if(m.some(y=>y.kind===\"cross-polymer\"||y.kind===\"hbond\"))throw new j(\"gap-at-complex-junction\",`Gap atom ${c} participates in a cross-polymer/hbond bond`,{atomId:c});let h=m.filter(y=>y.kind===\"backbone\");if(h.length>2)throw new j(\"gap-at-complex-junction\",`Gap atom ${c} has ${h.length} backbone bonds (max 2 allowed)`,{atomId:c,bondCount:h.length})}let o=i.atoms.filter(c=>!t.has(c.id)),r=[],s=[];for(let c of i.chains){let m=c.backboneAtoms.filter(y=>!t.has(y.id)),p=(()=>{let y=0;for(let f of i.bonds)f.id>y&&(y=f.id);return y+1})(),h=[];for(let y of c.bonds)t.has(y.a1.id)||t.has(y.a2.id)||h.push(y);for(let y=0;y<c.backboneAtoms.length;y++){let f=c.backboneAtoms[y];if(!t.has(f.id))continue;let _=Lr(c.backboneAtoms,y,t),b=Br(c.backboneAtoms,y,t);if(_===null||b===null)continue;let A={id:p++,a1:_,a2:b,kind:\"backbone\",r1:{kind:\"numeric\",r:2},r2:{kind:\"numeric\",r:1}};h.find(k=>k.a1.id===_.id&&k.a2.id===b.id)===void 0&&h.push(A);}for(let y of h)s.push(y);r.push({id:c.id,polymerType:c.polymerType,backboneAtoms:m,bonds:h,...c.annotation!==void 0?{annotation:c.annotation}:{}});}for(let c of i.bonds)c.kind!==\"cross-polymer\"&&c.kind!==\"hbond\"||t.has(c.a1.id)||t.has(c.a2.id)||s.push(c);let a=new Map;for(let c of r){let m=0;for(let p of c.backboneAtoms)m+=1,a.set(p.id,{...p,bio:{...p.bio,positionInChain:m}});}for(let c of o)a.has(c.id)||a.set(c.id,c);let d=r.map(c=>{let m=c.backboneAtoms.map(h=>a.get(h.id)),p=c.bonds.map(h=>({...h,a1:a.get(h.a1.id),a2:a.get(h.a2.id)}));return {id:c.id,polymerType:c.polymerType,backboneAtoms:m,bonds:p,...c.annotation!==void 0?{annotation:c.annotation}:{}}}),l=s.map(c=>({...c,a1:a.get(c.a1.id),a2:a.get(c.a2.id)}));return {mol:{atoms:o.map(c=>a.get(c.id)),bonds:l,chains:d,groups:i.groups,annotations:i.annotations},survivorByOldContinuousId:e}}function Lr(i,e,t){for(let n=e-1;n>=0;n--){let o=i[n];if(o!==void 0&&!t.has(o.id))return o}return null}function Br(i,e,t){for(let n=e+1;n<i.length;n++){let o=i[n];if(o!==void 0&&!t.has(o.id))return o}return null}function wn(i,e,t){let n=t?.mode??\"lenient\",o=[];for(let s of Rr)o.push(...s(i,e));let r=n===\"pedantic\"?o.map(s=>s.severity===\"warning\"?{...s,severity:\"error\"}:s):o;if(n===\"strict\"||n===\"pedantic\"){let s=r.filter(a=>a.severity===\"error\");if(s.length>0)throw new Ze(s)}return r}var Rr=[Ir,Pr,Hr,$r,Dr,Nr,Fr,Gr];function Ir(i,e){let t=[],n=new Set(i.chains.map(s=>s.id));for(let s of i.bonds)s.kind!==\"cross-polymer\"&&s.kind!==\"hbond\"||(n.has(s.a1.bio.chainId)||t.push({severity:\"error\",code:\"unknown-chain-reference\",message:`Connection references unknown chain '${s.a1.bio.chainId}'`,context:{chainId:s.a1.bio.chainId,bondId:s.id}}),n.has(s.a2.bio.chainId)||t.push({severity:\"error\",code:\"unknown-chain-reference\",message:`Connection references unknown chain '${s.a2.bio.chainId}'`,context:{chainId:s.a2.bio.chainId,bondId:s.id}}));for(let s of i.chains)for(let a of i.bonds){if(a.kind!==\"cross-polymer\"&&a.kind!==\"hbond\")continue;let d=0;for(let l of s.backboneAtoms)d+=l.branchAtom!==void 0?2:1;for(let l of [a.a1,a.a2]){if(l.bio.chainId!==s.id)continue;let u=le(l,s);(u<1||u>d)&&t.push({severity:\"error\",code:\"position-out-of-range\",message:`Position ${u} out of range for chain '${s.id}' (length ${d})`,context:{chainId:s.id,atomId:l.id,found:u}});}}let o=new Set;for(let s of i.groups)s.kind!==\"bracket\"&&o.add(s.id);for(let s of i.groups)if(s.kind!==\"bracket\")for(let a of s.members)n.has(a.target)||o.has(a.target)||t.push({severity:\"error\",code:\"unknown-group-reference\",message:`Group '${s.id}' references unknown id '${a.target}'`,context:{found:a.target}});let r=new Map;for(let s of i.groups){if(s.kind===\"bracket\")continue;let a=[];for(let d of s.members)o.has(d.target)&&a.push(d.target);r.set(s.id,a);}for(let s of r.keys()){let a=new Set,d=[s];for(;d.length>0;){let l=d.pop();if(a.has(l))continue;a.add(l);let u=r.get(l)??[];for(let c of u)c===s?t.push({severity:\"error\",code:\"group-cycle\",message:`Group cycle detected involving '${s}'`,context:{found:s}}):a.has(c)||d.push(c);}}return t}function Pr(i,e){let t=[];if(e===null)return t;let n=new Map;for(let o of i.chains)n.set(o.id,o.polymerType);for(let o of i.atoms){let r=n.get(o.bio.chainId);if(r===void 0)continue;let s=o.monomer,a=s?.meta;if(s===null||a?.missing===true){t.push({severity:\"warning\",code:\"unresolved-monomer\",message:`Monomer '${o.symbol}' not found in library for ${r}`,context:{chainId:o.bio.chainId,atomId:o.id,found:o.symbol}});continue}a?.ambiguous!==true&&s.smiles!==void 0&&s.smiles.length>0&&(s.rgroups.length===0?t.push({severity:\"warning\",code:\"inline-smiles-without-r-groups\",message:`Inline-SMILES monomer '${s.symbol}' has no R-groups`,context:{atomId:o.id,found:s.symbol}}):s.rgroups.length>4&&t.push({severity:\"warning\",code:\"inline-smiles-too-many-rs\",message:`Inline-SMILES monomer '${s.symbol}' has ${s.rgroups.length} R-groups (max 4 expected)`,context:{atomId:o.id,found:s.rgroups.length}}));}for(let o of i.atoms){let r=n.get(o.bio.chainId);if(!(r===void 0||e.getMonomer(r,o.symbol)!==null)){for(let a of e.getMonomerSymbolsByType(r))if(a!==o.symbol&&a.toLowerCase()===o.symbol.toLowerCase()){t.push({severity:\"info\",code:\"case-mismatch\",message:`Symbol '${o.symbol}' differs from library entry '${a}' only in case`,context:{atomId:o.id,found:o.symbol,expected:a}});break}}}return t}function Hr(i,e){let t=[],n=new Map;for(let o of i.bonds)for(let[r,s]of [[o.a1,o.r1],[o.a2,o.r2]]){if(s.kind!==\"numeric\")continue;let a=n.get(r.id)??new Set;a.has(s.r)&&t.push({severity:\"error\",code:\"rgroup-already-bonded\",message:`R-group R${s.r} on atom ${r.id} already bonded`,context:{atomId:r.id,bondId:o.id,found:s.r}}),a.add(s.r),n.set(r.id,a);}for(let o of i.bonds){for(let[r,s]of [[o.a1,o.r1],[o.a2,o.r2]]){if(s.kind!==\"numeric\"||r.monomer===null)continue;let a=r.monomer.rs;(s.r<1||s.r>a)&&t.push({severity:\"error\",code:\"rgroup-not-on-monomer\",message:`R-group R${s.r} not defined on monomer '${r.symbol}' (rs=${a})`,context:{atomId:r.id,bondId:o.id,found:s.r,expected:`R1..R${a}`}});}o.kind===\"backbone\"&&o.r1.kind===\"numeric\"&&o.r2.kind===\"numeric\"&&(o.r1.r===2&&o.r2.r===1||t.push({severity:\"warning\",code:\"backbone-rgroup-misaligned\",message:`Backbone bond uses R${o.r1.r}->R${o.r2.r} (expected R2->R1)`,context:{bondId:o.id,found:`R${o.r1.r}->R${o.r2.r}`}})),o.kind===\"branch\"&&o.r1.kind===\"numeric\"&&o.r1.r!==3&&t.push({severity:\"warning\",code:\"branch-rgroup-misaligned\",message:`Branch bond uses R${o.r1.r} (expected R3 on parent)`,context:{bondId:o.id,found:`R${o.r1.r}`}});}for(let o of i.atoms){if(o.monomer===null)continue;let s=n.get(o.id)?.size??0;if(o.monomer.rs>s){let a=o.monomer.rs-s;a>0&&o.monomer.rs>0&&t.push({severity:\"info\",code:\"unmatched-r-group\",message:`Monomer '${o.symbol}' on atom ${o.id} has ${a} unused R-group(s); default cap applied`,context:{atomId:o.id,found:a}});}}return t}function $r(i,e){let t=[];for(let n of i.chains){if(n.polymerType===\"CHEM\"&&n.backboneAtoms.length>1&&t.push({severity:\"error\",code:\"chem-multiple-monomers\",message:`CHEM polymer '${n.id}' has ${n.backboneAtoms.length} monomers (expected 1)`,context:{chainId:n.id,found:n.backboneAtoms.length}}),n.polymerType===\"BLOB\")for(let o of n.backboneAtoms)o.bio.blobtype===void 0&&o.symbol!==\"Bead\"&&o.symbol!==\"Group\"&&t.push({severity:\"error\",code:\"blob-non-blob-symbol\",message:`BLOB '${n.id}' contains non-blob symbol '${o.symbol}'`,context:{chainId:n.id,atomId:o.id,found:o.symbol}});if(n.polymerType===\"RNA\"){let o=false;for(let r=0;r<n.backboneAtoms.length;r++){let s=n.backboneAtoms[r];s.biotype===g.BASE&&!o&&t.push({severity:\"error\",code:\"rna-bare-base\",message:`Bare base '${s.symbol}' without parent sugar in '${n.id}'`,context:{chainId:n.id,atomId:s.id}}),s.biotype===g.LINKER&&(n.backboneAtoms.slice(0,r).some(d=>d.biotype===g.SUGAR)||t.push({severity:\"warning\",code:\"rna-bare-linker\",message:`Bare linker '${s.symbol}' before any sugar in '${n.id}'`,context:{chainId:n.id,atomId:s.id}})),o=s.biotype===g.SUGAR||s.biotype===g.LINKER;}}}return t}function Dr(i,e){let t=[],n=new Map;for(let r of i.chains)n.set(r.id,r.polymerType);let o=new Map;for(let r of i.bonds){if(r.kind!==\"hbond\")continue;o.set(r.a1.id,(o.get(r.a1.id)??0)+1),o.set(r.a2.id,(o.get(r.a2.id)??0)+1);let s=n.get(r.a1.bio.chainId),a=n.get(r.a2.bio.chainId);(s!==\"RNA\"||a!==\"RNA\")&&t.push({severity:\"error\",code:\"pair-non-rna\",message:`Hydrogen-bond connects non-RNA chains (${s}/${a})`,context:{bondId:r.id}}),(r.a1.biotype!==g.BASE||r.a2.biotype!==g.BASE)&&t.push({severity:\"warning\",code:\"pair-position-not-base\",message:\"Hydrogen-bond endpoints are not both bases\",context:{bondId:r.id,found:`${r.a1.biotype}/${r.a2.biotype}`}}),Or(r.a1.symbol,r.a2.symbol)||t.push({severity:\"warning\",code:\"pair-non-canonical\",message:`Non-canonical pair ${r.a1.symbol}-${r.a2.symbol}`,context:{bondId:r.id,found:`${r.a1.symbol}-${r.a2.symbol}`}});}for(let[r,s]of o)s>1&&t.push({severity:\"warning\",code:\"pair-already-paired\",message:`Base atom ${r} participates in ${s} pair bonds`,context:{atomId:r,found:s}});return t}function Or(i,e){let t=i.toUpperCase(),n=e.toUpperCase();return new Set([\"A:T\",\"T:A\",\"A:U\",\"U:A\",\"G:C\",\"C:G\"]).has(`${t}:${n}`)}function Nr(i,e){let t=[];for(let n of i.atoms){let o=n.bio.ambiguity;if(o!==void 0){if(n.bio.ambiguityKind===\"and\"){let r=ko(o,\"+\");for(let s of r)s.ratio!==void 0&&s.ratio<0&&t.push({severity:\"error\",code:\"ratio-and-negative\",message:`AND ratio for '${s.symbol}' is negative (${s.ratio})`,context:{atomId:n.id,found:s.ratio}});}else if(n.bio.ambiguityKind===\"or\"){let r=ko(o,\",\"),s=0,a=false;for(let d of r)typeof d.ratio==\"number\"&&(s+=d.ratio,a=true);a&&Math.abs(s-1)>.001&&Math.abs(s-100)>.5&&t.push({severity:\"info\",code:\"ratio-doesnt-sum-to-1\",message:`OR ratios sum to ${s} (expected 1.0 or 100)`,context:{atomId:n.id,found:s}});}}}return t}function ko(i,e){let t=i.trim();t.startsWith(\"(\")&&t.endsWith(\")\")&&(t=t.slice(1,-1));let n=t.split(e),o=[];for(let r of n){let s=r.trim();if(s.length===0)continue;let a=s.indexOf(\":\");if(a<0){o.push({symbol:s});continue}let d=s.slice(0,a),l=s.slice(a+1),u=parseFloat(l);Number.isFinite(u)?o.push({symbol:d,ratio:u}):o.push({symbol:d});}return o}function Fr(i,e){let t=[],n=new Set(i.chains.map(o=>o.id));for(let o of i.annotations.perPolymer.keys())n.has(o)||t.push({severity:\"warning\",code:\"annotation-unknown-polymer\",message:`Annotation references unknown polymer '${o}'`,context:{found:o}});return t}function Gr(i,e){let t=[];for(let o of i.chains)o.backboneAtoms.length>1e4&&t.push({severity:\"info\",code:\"polymer-too-long\",message:`Polymer '${o.id}' has ${o.backboneAtoms.length} atoms (> 10000); renderer may switch to rows layout`,context:{chainId:o.id,found:o.backboneAtoms.length}});let n=0;for(let o of i.bonds)(o.kind===\"cross-polymer\"||o.kind===\"hbond\")&&(n+=1);n>1e3&&t.push({severity:\"info\",code:\"connection-count-high\",message:`${n} cross-polymer/hbond connections (> 1000); rendering may be slow`,context:{found:n}});for(let o of i.groups)o.kind===\"bracket\"&&o.repeat!==void 0&&o.repeat.max>1e4&&t.push({severity:\"warning\",code:\"bracket-repeat-too-large\",message:`Bracket repeat upper bound ${o.repeat.max} > 10000`,context:{found:o.repeat.max}});return t}function Ao(i){let e=[];for(let s of i.chains){let a=jr(s.polymerType),d=s.backboneAtoms,l=[],u=[],c=[];for(let m of s.bonds)m.kind===\"backbone\"&&c.push(m);for(let m of d){if(m.biotype!==g.SUGAR){l.push(null),u.push(null);continue}let p=null,h=null;for(let y of s.bonds){if(y.kind!==\"branch\")continue;let f=y.a1.id===m.id?y.a2:y.a2.id===m.id?y.a1:null;if(f!==null&&f.biotype===g.BASE){p=f,h=y;break}}l.push(p),u.push(h);}e.push({id:s.id,polymerType:a,backbone:d,bases:l,backboneBonds:c,baseBonds:u,...s.strandType!==void 0?{strandType:s.strandType}:{}});}let t=zr(e,i),n=new Set,o=t.map(s=>{let a=s[0].id;for(let d=2;n.has(a);d++)a=`${s[0].id}#${d}`;return n.add(a),a}),r=new Map;return t.forEach((s,a)=>{for(let d of s)for(let l of d.backbone)r.set(l.id,o[a]),l.branchAtom!==void 0&&r.set(l.branchAtom.id,o[a]);}),t.map((s,a)=>Vr(s,o[a],i,r))}function Vr(i,e,t,n){let o=[],r=[],s=[],a=[];for(let l of i)o.push(...l.backbone),r.push(...l.bases),s.push(...l.backboneBonds),a.push(...l.baseBonds);let d=i.find(l=>l.strandType!==void 0)?.strandType;return {id:e,polymerType:Ur(i),segments:i.map(l=>l.id),backbone:o,bases:r,backboneBonds:s,baseBonds:a,isCyclic:qr(t,e,o,n),...d!==void 0?{strandType:d}:{}}}function Ur(i){let e=new Map;for(let o of i)e.set(o.polymerType,(e.get(o.polymerType)??0)+o.backbone.length);let t=i[0].polymerType,n=-1;for(let o of i){let r=e.get(o.polymerType);r>n&&(t=o.polymerType,n=r);}return t}function zr(i,e){let t=new Map;i.forEach((l,u)=>{for(let c of l.backbone)t.set(c.id,u);});let n=new Map,o=new Map;for(let l of e.bonds){if(l.kind!==\"cross-polymer\")continue;let u=Kr(l,i,t);if(u===null)continue;let{tail:c,head:m}=u;c!==m&&(n.has(c)||o.has(m)||Wr(n,m,c)||(n.set(c,m),o.set(m,c)));}let r=[],s=new Set;for(let l=0;l<i.length;l++){if(s.has(l)||o.has(l))continue;let u=[],c=l;for(;c!==void 0&&!s.has(c);)s.add(c),u.push(i[c]),c=n.get(c);r.push(u);}for(let l=0;l<i.length;l++)s.has(l)||(s.add(l),r.push([i[l]]));let a=new Map;i.forEach((l,u)=>a.set(l,u));let d=l=>Math.min(...l.map(u=>a.get(u)));return r.sort((l,u)=>d(l)-d(u))}function Kr(i,e,t){let n=(r,s)=>r.kind===\"numeric\"&&r.r===s,o=[[i.a1,i.r1,i.a2,i.r2],[i.a2,i.r2,i.a1,i.r1]];for(let[r,s,a,d]of o){if(!n(s,2)||!n(d,1))continue;let l=t.get(r.id),u=t.get(a.id);if(l===void 0||u===void 0)continue;let c=e[l],m=e[u];if(c.backbone[c.backbone.length-1].id===r.id&&m.backbone[0].id===a.id)return {tail:l,head:u}}return null}function Wr(i,e,t){let n=new Set,o=e;for(;o!==void 0&&!n.has(o);){if(o===t)return  true;n.add(o),o=i.get(o);}return  false}function jr(i){switch(i){case x.PEPTIDE:return \"PEPTIDE\";case x.RNA:return \"RNA\";case x.CHEM:return \"CHEM\";case x.BLOB:return \"BLOB\";default:return \"BLOB\"}}function qr(i,e,t,n){if(t.length<2)return  false;let o=t[0],r=t[t.length-1];for(let s of i.bonds){if(s.kind===\"backbone\"||s.kind===\"branch\")continue;let a=n.get(s.a1.id),d=n.get(s.a2.id);if(a!==e||d!==e||!(s.a1.id===r.id&&s.a2.id===o.id||s.a2.id===r.id&&s.a1.id===o.id))continue;let u=s.a1.id===o.id?s.r1:s.r2,c=s.a1.id===r.id?s.r1:s.r2,m=u.kind===\"numeric\"&&u.r===1,p=c.kind===\"numeric\"&&c.r===2;if(m&&p)return  true}return  false}var kn=44.800000000000004,Mo=1.5*28,Tt=1.5*28/kn,An=1.5*28/kn,Mn=1.5*28/kn;function Ae(i,e){let t=e?.bondLength??28,n=e?.origin??{x:0,y:0},o=1.6*t,r=new Map;for(let s=0;s<i.backbone.length;s++){let a=i.backbone[s];r.set(a.id,{x:n.x+s*o,y:n.y});}return r}var Yr=Math.PI/180;function St(i,e){let t=i.backbone.length;if(t<=2){let l={};return e?.bondLength!==void 0&&(l.bondLength=e.bondLength),e?.origin!==void 0&&(l.origin=e.origin),Ae(i,l)}let n=e?.bondLength??28,o=e?.origin??{x:0,y:0},r=e?.startDegrees??-90,a=1.6*n/(2*Math.sin(Math.PI/t)),d=new Map;for(let l=0;l<t;l++){let u=i.backbone[l],m=(r+l*360/t)*Yr;d.set(u.id,{x:o.x+a*Math.cos(m),y:o.y+a*Math.sin(m)});}return d}var Xr=10,Jr=1.5/1.6;function To(i,e){let t=e?.bondLength??28,n=e?.origin??{x:0,y:0},o=Math.max(1,e?.perRow??Xr),r=e?.rowSpacing??Jr,s=1.6*t,a=r*s,d=new Map;for(let l=0;l<i.backbone.length;l++){let u=i.backbone[l],c=Math.floor(l/o),m=l%o,p=c%2===0?n.x+m*s:n.x+(o-1-m)*s,h=n.y+c*a;d.set(u.id,{x:p,y:h});}return d}function So(i,e){let t=new Map;for(let r=0;r<i.backbone.length;r++)t.set(i.backbone[r].id,r);let n=i.backbone.length-1,o=[];for(let r of e.bonds){if(r.kind===\"backbone\"||r.kind===\"branch\")continue;let s=t.get(r.a1.id),a=t.get(r.a2.id);if(s===void 0||a===void 0)continue;let d=Math.min(s,a),l=Math.max(s,a);l-d<2||d===0&&l===n&&Zr(r)||o.push({lo:d,hi:l});}return o}function Zr(i){let t=[i.r1,i.r2].filter(n=>n.kind===\"numeric\").map(n=>n.r);return t.length===2&&t.includes(1)&&t.includes(2)}function Eo(i,e){return e===null?false:So(i,e).length>0}function Tn(i,e,t){if(e===null)return Ae(i,t);let n=t?.bondLength??28,o=t?.origin??{x:0,y:0},r=1.6*n,s=So(i,e);if(s.length===0)return Ae(i,t);let a=s[0].lo,d=s[0].hi;for(let E of s)E.lo<a&&(a=E.lo),E.hi>d&&(d=E.hi);let l=i.backbone.slice(a,d+1),u=l.length,c=r/(2*Math.sin(Math.PI/u)),m={id:i.id,polymerType:i.polymerType,segments:i.segments,backbone:l,bases:new Array(u).fill(null),baseBonds:new Array(u).fill(null)},p=a,h={x:o.x+p*r+c,y:o.y},y=St(m,{bondLength:n,origin:h,startDegrees:180}),f=new Map;for(let E=0;E<a;E++){let H=i.backbone[E];f.set(H.id,{x:o.x+E*r,y:o.y});}for(let[E,H]of y)f.set(E,H);let _=l[u-1],b=y.get(_.id)??h,A=b.x-h.x,w=b.y-h.y,k=Math.hypot(A,w);k<1e-6&&(A=0,w=1,k=1);let C=A/k,I=w/k,T={x:b.x+C*r,y:b.y+I*r},B=Math.sign(b.x-h.x);if(B===0&&u>=2){let E=y.get(l[u-2].id);E!==void 0&&(B=Math.sign(b.x-E.x));}B===0&&(B=1);for(let E=d+1;E<i.backbone.length;E++){let H=i.backbone[E],_e=E-(d+1);f.set(H.id,_e===0?T:{x:T.x+B*r*_e,y:T.y});}return f}function Lo(i){let e=new Map,t=new Map;for(let n=0;n<i.backbone.length;n++){e.set(i.backbone[n].id,n);let o=i.bases[n];o!=null&&t.set(o.id,n);}return {sugarToIdx:e,baseToIdx:t}}function Co(i,e,t){let n=e.get(i);if(n!==void 0)return n;let o=t.get(i);return o!==void 0?o:null}function Bo(i,e,t){let n=i.kind===\"hbond\",o=i.kind===\"cross-polymer\"&&typeof i.r1==\"object\"&&i.r1!==null&&i.r1.kind===\"pair\"&&typeof i.r2==\"object\"&&i.r2!==null&&i.r2.kind===\"pair\";if(!n&&!o)return null;let r=Co(i.a1.id,e,t),s=Co(i.a2.id,e,t);return r===null||s===null||r===s?null:{lo:Math.min(r,s),hi:Math.max(r,s)}}function Ro(i,e){if(i.polymerType!==\"RNA\"||i.backbone.length===0)return  false;let{sugarToIdx:t,baseToIdx:n}=Lo(i);for(let o of e.bonds)if(Bo(o,t,n)!==null)return  true;return  false}function Qr(i,e){let t=i.backbone.length,n=new Int32Array(t).fill(-1);if(t===0)return n;let{sugarToIdx:o,baseToIdx:r}=Lo(i),s=[];for(let d of e.bonds){let l=Bo(d,o,r);l!==null&&s.push([l.lo,l.hi]);}s.sort((d,l)=>d[0]-l[0]||l[1]-d[1]);let a=[];for(let d of s){let[l,u]=d,c=false;for(let[m,p]of a){let h=u<m||l>p,y=l>m&&u<p||l<m&&u>p;if(!h&&!y){c=true;break}}c||n[l]!==-1||n[u]!==-1||(n[l]=u,n[u]=l,a.push(d));}return n}function es(i){return e(0,i.length-1,null);function e(t,n,o){let r=[],s=-1,a=t;for(;a<=n;){let d=i[a];if(d>a&&d<=n){s!==-1&&(r.push({kind:\"unpaired\",from:s,to:a-1}),s=-1);let l=1;for(;a+2*l<d-2*l&&i[a+2*l]===d-2*l&&i[a+2*l-1]===-1&&i[d-2*l+1]===-1;)l+=1;let u=a+2*(l-1),c=d-2*(l-1),m=[u,c],p=e(u+1,c-1,m);r.push({kind:\"stem\",fromIdx:a,toIdx:d,numPairs:l,child:p}),a=d+1;}else s===-1&&(s=a),a+=1;}return s!==-1&&r.push({kind:\"unpaired\",from:s,to:n}),{kind:\"loop\",nodes:r,closingPair:o}}}function Et(i){let e=Math.hypot(i.x,i.y);return e===0?{x:1,y:0}:{x:i.x/e,y:i.y/e}}function ts(i){return {x:-i.y,y:i.x}}function Sn(i,e,t){return {x:i.x+e*Math.cos(t),y:i.y+e*Math.sin(t)}}function ns(i,e,t,n){let o=t+n+1;if(o<=0)return Math.max(i/2+1,e);let r=n+1,s=o*e,a=Math.max(s/(2*Math.PI),i/2+1);for(let d=0;d<64;d++){let l=i/(2*a),c=2*Math.asin(Math.min(.9999,Math.max(-0.9999,l))),m=(2*Math.PI-r*c)*a-s,p=l,h=Math.sqrt(Math.max(1e-12,1-p*p)),f=2*(-i/(2*a*a)/h),_=2*Math.PI-r*c-r*a*f;if(!Number.isFinite(_)||Math.abs(_)<1e-12)break;let b=m/_,A=a-b;if(!Number.isFinite(A)||A<i/2+.001){a=i/2+.001;break}if(a=A,Math.abs(b)<1e-9)break}return Math.max(a,i/2+.001)}function Ct(i,e,t,n,o){let r=o.chain.bases[i];r!=null&&o.out.set(r.id,{x:e.x+n*t.x,y:e.y+n*t.y});}function Io(i,e,t){let{chain:n,step:o,rail:r,baseInwardHang:s,out:a}=t,d=2*i.numPairs-1,l={x:e.normal.x,y:e.normal.y},u={x:-e.normal.x,y:-e.normal.y};for(let m=0;m<d;m++){let p=n.backbone[i.fromIdx+m],h=n.backbone[i.toIdx-m],y=m*o,f={x:e.origin.x+y*e.tangent.x,y:e.origin.y+y*e.tangent.y},_={x:e.origin.x+y*e.tangent.x+r*e.normal.x,y:e.origin.y+y*e.tangent.y+r*e.normal.y};a.set(p.id,f),a.set(h.id,_),Ct(i.fromIdx+m,f,l,s,t),Ct(i.toIdx-m,_,u,s,t);}let c=(d-1)*o;return {origin:{x:e.origin.x+c*e.tangent.x,y:e.origin.y+c*e.tangent.y},tangent:e.tangent,normal:e.normal}}function Po(i,e,t,n){if(i.closingPair===null)return;let{step:o,rail:r,out:s}=t,a=0,d=0;for(let C of i.nodes)C.kind===\"unpaired\"?a+=C.to-C.from+1:d+=1;let l=ns(r,o,a,d),u=s.get(t.chain.backbone[i.closingPair[0]].id),c=s.get(t.chain.backbone[i.closingPair[1]].id),m={x:(u.x+c.x)/2,y:(u.y+c.y)/2},p=Math.sqrt(Math.max(0,l*l-r/2*(r/2))),h={x:m.x+p*e.tangent.x,y:m.y+p*e.tangent.y},y=Math.atan2(u.y-h.y,u.x-h.x),_=Math.atan2(c.y-h.y,c.x-h.x)-y;for(;_>Math.PI;)_-=2*Math.PI;for(;_<=-Math.PI;)_+=2*Math.PI;let b=_>0?-1:1,A=2*Math.asin(Math.min(.9999,Math.max(-0.9999,r/(2*l)))),w=o/l,k=y;for(let C of i.nodes)if(C.kind===\"unpaired\")for(let I=C.from;I<=C.to;I++){k=k+b*w;let T=Sn(h,l,k);s.set(t.chain.backbone[I].id,T);let B=Et({x:T.x-h.x,y:T.y-h.y});Ct(I,T,B,t.step,t);}else {k=k+b*w;let I=Sn(h,l,k);k=k+b*A;let T=Sn(h,l,k);s.set(t.chain.backbone[C.fromIdx].id,I),s.set(t.chain.backbone[C.toIdx].id,T);let B=Et({x:(I.x+T.x)/2-h.x,y:(I.y+T.y)/2-h.y}),E=Et({x:T.x-I.x,y:T.y-I.y}),_e=Io(C,{origin:I,tangent:B,normal:E},t);Po(C.child,_e,t);}}function os(i,e,t){let{step:n,rail:o,out:r}=t,s={x:e.origin.x,y:e.origin.y},a={x:e.tangent.x,y:e.tangent.y},d={x:-e.normal.x,y:-e.normal.y};for(let l of i.nodes)if(l.kind===\"unpaired\")for(let u=l.from;u<=l.to;u++){let c={x:s.x,y:s.y};r.set(t.chain.backbone[u].id,c),Ct(u,c,{x:e.normal.x,y:e.normal.y},t.step,t),s={x:s.x+n*a.x,y:s.y+n*a.y};}else {let u={origin:{x:s.x,y:s.y},tangent:d,normal:a},c=Io(l,u,t);Po(l.child,c,t),s={x:s.x+(o+n)*a.x,y:s.y+(o+n)*a.y};}}function Ho(i,e,t){let n=t?.bondLength??28,o=1.6*n,r=o/2,a=Mo*(n/28)+2*r,d=t?.origin??{x:0,y:0},l=Et(t?.rootDirection??{x:1,y:0}),u=ts(l),c=new Map;if(i.backbone.length===0)return c;let m=Qr(i,e),p=es(m);os(p,{origin:d,tangent:l,normal:u},{chain:i,step:o,rail:a,baseInwardHang:r,out:c});for(let f of i.backbone)c.has(f.id)||c.set(f.id,{x:d.x,y:d.y});return c}function $o(i,e,t){let n=t?.bondLength??28,o=1.6*n;for(let r=0;r<i.backbone.length;r++){let s=i.bases[r];if(s==null||e.has(s.id))continue;let a=i.backbone[r],d=e.get(a.id);if(d===void 0)continue;let l=is(i,r,e);e.set(s.id,{x:d.x+o*l.x,y:d.y+o*l.y});}return e}function is(i,e,t){let n=i.backbone[e],o=t.get(n.id);if(o===void 0)return {x:0,y:1};let r=e>0?i.backbone[e-1]:void 0,s=e<i.backbone.length-1?i.backbone[e+1]:void 0,a=r!==void 0?t.get(r.id):void 0,d=s!==void 0?t.get(s.id):void 0,l=y=>{let f=y.x-o.x,_=y.y-o.y,b=Math.hypot(f,_);return b<1e-9?null:{x:f/b,y:_/b}},u=a!==void 0?l(a):null,c=d!==void 0?l(d):null;if(u!==null&&c!==null){let y=u.x+c.x,f=u.y+c.y,_=Math.hypot(y,f);if(_>.05)return {x:-y/_,y:-f/_}}let m=c??u;if(m===null)return {x:0,y:1};let p={x:m.y,y:-m.x},h={x:-m.y,y:m.x};return p.y>=h.y?p:h}var rs=.72,ss=.45;function Go(i,e,t,n){let o=n?.bondLength??28,r=1.6*o,s=new Map,a=new Map;for(let f of i){let _=new Set;for(let b of f.backbone)_.add(b.id);for(let b of f.bases)b!==null&&_.add(b.id);a.set(f.id,{chain:f,atomIds:_});for(let b of _)s.set(b,f);}let d=new Map;for(let f of t.bonds)for(let _ of [f.a1,f.a2]){let b=d.get(_.id);b===void 0?d.set(_.id,[f]):b.push(f);}let l=new Set;if(i.length>0){let f=i.find(_=>_.strandType===\"ss\");l.add((f??i[0]).id);}let u=new Map;for(let f of i)u.set(f.id,f.id);let c=f=>{let _=f;for(;u.get(_)!==_;)_=u.get(_);let b=f;for(;u.get(b)!==_;){let A=u.get(b);u.set(b,_),b=A;}return _},m=(f,_)=>{u.set(c(f),c(_));},p=f=>{let _=c(f),b=0;for(let A of u.keys())c(A)===_&&(b+=1);return b},h=f=>{let _=s.get(f),b=_===void 0?void 0:c(_.id);return A=>{let w=s.get(A);return w!==void 0&&b!==void 0&&c(w.id)===b}},y=f=>{let _=c(f),b=new Set;for(let[A,w]of a)if(c(A)===_)for(let k of w.atomIds)b.add(k);return b};for(let f of t.bonds){if(f.kind===\"backbone\"||f.kind===\"branch\")continue;let _=s.get(f.a1.id),b=s.get(f.a2.id);if(_===void 0||b===void 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Zn={fixedAtomId:ee.id,fixedPos:on,movingAtomId:Se.id},Qn=En(l,a),Ji=Fo(H,Zn,t,Qn,e,h(ee.id));No(H,nn,ee,Zn,Ji,d,Qn,r,e)||ds(H,nn,_e,on,r,e);}m(_.id,b.id);continue}let C=e.get(w.id),I=e.get(k.id);if(!(C===void 0||I===void 0)){if(f.kind===\"hbond\"){let T=a.get(A.id);as(T.atomIds,e),ls(T.atomIds,e);let B=e.get(k.id),E=C.x-B.x,H=C.y+r*An-B.y;H=Do(H,T,l,a,e,r*An),He(T.atomIds,e,E,H);}else {let T=a.get(A.id),B=En(l,a),E={fixedAtomId:w.id,fixedPos:C,movingAtomId:k.id},H=Fo(T.atomIds,E,t,B,e,h(w.id));if(A.isCyclic&&A.backbone.length>=3&&H.length===1){let Se=A.id===_.id?b:_,ee=a.get(Se.id);_s(T.atomIds,I,ee.atomIds,C,r,e),l.add(A.id),m(_.id,b.id);continue}if(!No(T.atomIds,I,w,E,H,d,B,r,e)){let Se=C.x-I.x,ee=C.y+r*Mn-I.y;ee=Do(ee,T,l,a,e,r*Mn),He(T.atomIds,e,Se,ee);}}l.add(A.id),m(_.id,b.id);}}return l}function Do(i,e,t,n,o,r){let s=Vo(e.atomIds,o);if(s===null)return i;let a=null;for(let u of t){let c=n.get(u);if(c===void 0)continue;let 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Ys(i,e,t,n){i.save(),i.fillStyle=t.annotationColor,i.font=`${n*.7}px ${t.fontFamily}`,i.textAlign=\"left\",i.textBaseline=\"alphabetic\";for(let r of e.atoms){let s=r.bio.annotation;if(s===void 0||s===\"\")continue;let a=he(r,t);i.fillText(s,r.p.x+a.size+2,r.p.y-a.size);}i.font=`${n*.8}px ${t.fontFamily}`;for(let r of e.chains){if(r.annotation===void 0||r.annotation===\"\")continue;let s=r.backboneAtoms[0];s!==void 0&&i.fillText(r.annotation,s.p.x,s.p.y-t.fontSize*1.4);}i.font=`bold ${n*.85}px ${t.fontFamily}`,i.textAlign=\"center\",i.textBaseline=\"middle\";let o=t.fontSize*1.4;for(let r of e.chains){if(r.polymerType!==\"RNA\")continue;let s=r.backboneAtoms;if(s.length<2)continue;let a=s[0],d=s[s.length-1],l=s.length>=2?s[1]:null,u=s.length>=2?s[s.length-2]:null,c=si(a.p,l?.p??null,o),m=si(d.p,u?.p??null,o),p=r.strandType!==void 0?`5'${r.strandType}`:\"5'\",h=r.strandType!==void 0?`3'${r.strandType}`:\"3'\";i.fillText(p,c.x,c.y),i.fillText(h,m.x,m.y);}i.restore();}function si(i,e,t){if(e===null)return {x:i.x-t,y:i.y};let n=i.x-e.x,o=i.y-e.y,r=Math.hypot(n,o);return r===0?{x:i.x-t,y:i.y}:{x:i.x+t*(n/r),y:i.y+t*(o/r)}}function Xs(i,e,t,n,o=false,r=t.bondLength){for(let s of e.atoms){if(s.hidden)continue;let a=he(s,t),d=D(s.monomer,s.biotype,t.colorTheme);i.save(),i.fillStyle=d.background,i.strokeStyle=d.background,i.lineWidth=a.strokeWidth,i.lineJoin=\"round\",i.lineCap=\"round\",s.symbol===\"*\"?i.setLineDash([3,3]):i.setLineDash([]),Js(i,s,a.size,a.cornerRadius??0),i.fill(),i.stroke(),i.restore();let l=s.monomer?.symbol??s.symbol;if(l!==\"\"){let u=l.length<=1?1:Math.min(1,2/l.length),c=n*u;i.save(),i.fillStyle=d.text,i.font=`${c}px ${t.fontFamily}`,i.textAlign=\"center\",i.textBaseline=\"middle\",i.fillText(l,s.p.x,s.p.y),i.restore();}if(o){let u=r*Pn;i.save(),i.fillStyle=t.idColor,i.font=`${n*Hn}px ${t.fontFamily}`,i.textAlign=\"right\",i.textBaseline=\"bottom\",i.fillText(String(s.bio.continuousId),s.p.x-u,s.p.y-u),i.restore();}}}function Js(i,e,t,n){let o=e.p,r=e.symbol===\"*\"?\"circle\":It(e.biotype);switch(i.beginPath(),r){case \"hexagon\":ai(i,o,6,t,-30);break;case \"diamond\":i.moveTo(o.x,o.y-t),i.lineTo(o.x+t,o.y),i.lineTo(o.x,o.y+t),i.lineTo(o.x-t,o.y),i.closePath();break;case \"pentagon\":ai(i,o,5,t,-90);break;case \"rounded-rect\":case \"blob\":{let s=t/2,a=Math.max(0,Math.min(n,s)),d=o.x-s,l=o.y-s,u=s*2,c=s*2;i.moveTo(d+a,l),i.lineTo(d+u-a,l),i.quadraticCurveTo(d+u,l,d+u,l+a),i.lineTo(d+u,l+c-a),i.quadraticCurveTo(d+u,l+c,d+u-a,l+c),i.lineTo(d+a,l+c),i.quadraticCurveTo(d,l+c,d,l+c-a),i.lineTo(d,l+a),i.quadraticCurveTo(d,l,d+a,l),i.closePath();break}case \"circle\":i.ellipse(o.x,o.y,t,t,0,0,Math.PI*2);break}}function ai(i,e,t,n,o){let r=360/t;for(let s=0;s<t;s++){let a=(o+s*r)*Math.PI/180,d=e.x+n*Math.cos(a),l=e.y+n*Math.sin(a);s===0?i.moveTo(d,l):i.lineTo(d,l);}i.closePath();}function Zs(i,e){switch(i.kind){case \"backbone\":case \"branch\":return e.defaultStroke;case \"cross-polymer\":return e.crossPolymerBondColor;case \"hbond\":return ta(i)?e.hbondColor:e.nonCanonicalHbondColor;case \"group\":return e.defaultStroke}}function Qs(i){return $n}var ea=[[\"A\",\"T\"],[\"A\",\"U\"],[\"G\",\"C\"]];function ta(i){if(i.a1.biotype!==g.BASE||i.a2.biotype!==g.BASE)return  false;let e=li(i.a1),t=li(i.a2);for(let[n,o]of ea)if(e===n&&t===o||e===o&&t===n)return  true;return  false}function li(i){let e=i.monomer?.naturalAnalog,t=e!==void 0&&e!==\"\"?e:i.symbol;return t.length===0?\"\":t.charAt(0).toUpperCase()}function fe(i){let e=new Map,t=new Map;for(let o of i.bonds){let r=o.a1.id,s=o.a2.id,a=t.get(r);a===void 0&&(a=[],t.set(r,a)),a.push(o);let d=t.get(s);d===void 0&&(d=[],t.set(s,d)),d.push(o);}for(let o of i.atoms)ci(e,o,t.get(o.id)??[]);for(let o of i.groups){if(o.kind!==\"bracket\")continue;let r=o.repeat?.min??1;if(r===1)continue;let s=new Set(o.members.map(d=>d.target)),a=new Map;for(let d of i.atoms){if(!s.has(d.bio.chainId))continue;let l=new Map;ci(l,d,t.get(d.id)??[]);for(let[u,c]of l)a.set(u,(a.get(u)??0)+c*(r-1));}for(let[d,l]of a)e.set(d,(e.get(d)??0)+l);}for(let[o,r]of [...e])r===0&&e.delete(o);let n=ia(e);return {elements:e,mw:n}}var na={H:1.008,C:12.011,N:14.007,O:15.999,F:18.998,Na:22.99,Mg:24.305,P:30.974,S:32.06,Cl:35.45,K:39.098,Ca:40.078,Br:79.904,I:126.904,Fe:55.845,Zn:65.38,Cu:63.546},oa={C:4,N:3,O:2,S:2,P:3,F:1,Cl:1,Br:1,I:1,H:1};function ia(i){let e=0;for(let[t,n]of i){let o=na[t];o!==void 0&&(e+=o*n);}return Math.round(e*1e3)/1e3}function ci(i,e,t){if(e.monomer===null)return;let n=sa(e.monomer);for(let[o,r]of n.elements)i.set(o,(i.get(o)??0)+r);for(let o of t){if(o.kind===\"hbond\"||o.kind===\"group\")continue;let r=o.a1.id===e.id?o.r1:o.r2,s=ra(e.monomer,r);if(s===void 0)continue;let a=mi(s);for(let[d,l]of a)i.set(d,(i.get(d)??0)-l);}}function ra(i,e){if(e.kind!==\"numeric\"&&e.kind!==\"positional\")return;let t=(e.kind===\"numeric\",e.r);for(let n of i.rgroups){let o=/^R([1-9][0-9]*)$/.exec(n.label);if(o!==null&&parseInt(o[1],10)===t)return n.capGroupName}}function mi(i){let e=new Map;switch(i){case \"H\":e.set(\"H\",1);break;case \"OH\":e.set(\"H\",1),e.set(\"O\",1);break;}return e}var ui=new WeakMap;function sa(i){let e=ui.get(i);if(e!==void 0)return e;let t=aa(i);return ui.set(i,t),t}function aa(i){let e=new Map;if(i.molfile===void 0||i.molfile===\"\")return {elements:e};let t=la(i.molfile);if(t===null)return {elements:e};let{atoms:n,bondOrders:o}=t;for(let r=0;r<n.length;r++){let s=n[r];if(s===\"R\"||s===\"R#\"||s===\"*\")continue;e.set(s,(e.get(s)??0)+1);let a=oa[s];if(a===void 0)continue;let d=o[r]??0,l=a-d;l>0&&e.set(\"H\",(e.get(\"H\")??0)+l);}for(let r of i.rgroups){let s=r.capGroupName;if(s===void 0)continue;let a=mi(s);for(let[d,l]of a)e.set(d,(e.get(d)??0)+l);}return {elements:e}}function la(i){let e=i.split(/\\r\\n|\\n|\\r/);if(e.length<5)return null;let t=e[3];if(t===void 0||t.length<6)return null;let n=parseInt(t.slice(0,3),10),o=parseInt(t.slice(3,6),10);if(!Number.isFinite(n)||!Number.isFinite(o)||e.length<4+n+o)return null;let r=[];for(let a=0;a<n;a++){let d=e[4+a];if(d===void 0)return null;let l=d.slice(31,34).trim();r.push(l);}let s=new Array(n).fill(0);for(let a=0;a<o;a++){let d=e[4+n+a];if(d===void 0)return null;let l=parseInt(d.slice(0,3),10),u=parseInt(d.slice(3,6),10),c=parseInt(d.slice(6,9),10);if(!Number.isFinite(l)||!Number.isFinite(u)||!Number.isFinite(c))continue;let m=c===4?1:c;l>=1&&l<=n&&(s[l-1]=(s[l-1]??0)+m),u>=1&&u<=n&&(s[u-1]=(s[u-1]??0)+m);}return {atoms:r,bondOrders:s}}function De(i){return fe(i).mw}var Fn={W:5.5,Y:1.49,C:.0625},da={AA:13.65,AC:10.67,AG:12.79,AU:12.14,CA:10.67,CC:7.52,CG:9.39,CU:8.37,GA:12.79,GC:9.39,GG:11.77,GU:10.21,UA:12.14,UC:8.37,UG:10.21,UU:8.99},pi={A:15.4,C:7.4,G:11.7,U:10,T:8.8};function Oe(i){let e=0;for(let t of i.chains)t.polymerType===\"PEPTIDE\"?e+=ca(t.backboneAtoms):t.polymerType===\"RNA\"&&(e+=ua(t.backboneAtoms));return Math.round(e*1e4)/1e4}function ca(i){let e=0,t=0,n=0;for(let o of i){let r=hi(o);r===\"W\"?e++:r===\"Y\"?t++:r===\"C\"&&n++;}return Fn.W*e+Fn.Y*t+Fn.C*n}function ua(i){let e=[];for(let o of i)if(o.branchAtom!==void 0&&o.branchAtom.biotype===g.BASE){let r=hi(o.branchAtom);r===\"T\"&&(r=\"U\"),r!==\"\"&&e.push(r);}if(e.length===0)return 0;if(e.length===1){let o=e[0];return pi[o]??0}let t=0;for(let o=0;o<e.length-1;o++){let r=e[o],s=e[o+1],a=da[r+s];a!==void 0&&(t+=a);}let n=0;for(let o=1;o<e.length-1;o++){let r=e[o];n+=pi[r]??0;}return 2*t-n}function hi(i){let e=i.monomer;return e!==null&&e.naturalAnalog!==void 0&&e.naturalAnalog!==\"\"?e.naturalAnalog.charAt(0).toUpperCase():i.symbol===\"\"?\"\":i.symbol.charAt(0).toUpperCase()}function Dt(i){let e=[];e.push(\"HWE pseudo-molfile\"),e.push(\" HWE          2D\"),e.push(\"\");let t=i.atoms.length,n=i.bonds.length;e.push(ma(t,n));for(let r of i.atoms)e.push(pa(r));let o=new Map;for(let r=0;r<i.atoms.length;r++)o.set(i.atoms[r].id,r+1);for(let r of i.bonds){let s=o.get(r.a1.id),a=o.get(r.a2.id);s===void 0||a===void 0||e.push(ha(s,a));}return e.push(\"M  END\"),e.join(`\n`)+`\n`}function ma(i,e){return Ne(i)+Ne(e)+\"  0  0  0  0  0  0  0  0999 V2000\"}function pa(i){let e=fa(i);return Gn(i.p.x)+Gn(i.p.y)+Gn(0)+\" \"+ba(e,3)+\" 0  0  0  0  0  0  0  0  0  0  0  0\"}function ha(i,e){return Ne(i)+Ne(e)+Ne(1)+Ne(0)}function fa(i){let e=i.monomer;return e!==null&&e.symbol!==\"\"?e.symbol:i.symbol!==\"\"?i.symbol:e!==null&&e.naturalAnalog!==void 0&&e.naturalAnalog!==\"\"?e.naturalAnalog:\"X\"}function Ne(i){let e=String(i);return e.length>=3?e:\" \".repeat(3-e.length)+e}function ba(i,e){return i.length>=e?i:i+\" \".repeat(e-i.length)}function Gn(i){let e=i.toFixed(4);return e.length>=10?e.slice(0,10):\" \".repeat(10-e.length)+e}var ya=new Map;function ga(i){return `${i.mode}|${i.resolveMonomers?1:0}|${i.helm}`}function _a(i){let e=i.chains.map(o=>`${o.id}:${o.polymerType}:${o.backboneAtoms.length}`).join(\",\"),t=i.atoms.map(o=>`${o.id}@${o.symbol}@${o.bio.chainId}`).join(\";\"),n=i.bonds.map(o=>`${o.id}:${o.a1.id}-${o.a2.id}:${o.kind}`).join(\";\");return `${e}#${t}#${n}`}var va=256,Vn=class{constructor(e){this._destroyed=false;this._parseHits=0;this._parseMisses=0;this._layoutHits=0;this._layoutMisses=0;this._renderHits=0;this._renderMisses=0;if(e.monomerLib===void 0||e.monomerLib===null)throw new TypeError(\"HelmService: options.monomerLib is required\");this.monomerLib=e.monomerLib,this.theme=e.theme??$,this.logger=e.logger??new Ce,this.options=Object.freeze({...e});let t=e.cacheSize??va;this._parseCache=new Ee({max:t}),this._layoutCache=new Ee({max:t}),this._renderCache=new Ee({max:t}),this._libUnsub=this.monomerLib.onChanged.subscribe(()=>{this.clearCaches();});}parse(e,t){this._ensureLive(),e=this._normalizeHelm(e);let n=t?.mode??\"lenient\",o=t?.resolveMonomers!==false,r=ga({mode:n,resolveMonomers:o,helm:e}),s=this._parseCache.get(r);if(s!==void 0)return this._parseHits+=1,s;this._parseMisses+=1;let a={mode:n,resolveMonomers:o},d=ot(e,this.monomerLib,a),l={mol:d.mol,diagnostics:Object.freeze([...d.diagnostics])};return this._parseCache.set(r,l),l}serialize(e,t){this._ensureLive();let n={...t?.canonicalize!==void 0?{canonicalize:t.canonicalize}:{},...t?.includeHighlights!==void 0?{includeHighlights:t.includeHighlights}:{},...t?.version!==void 0?{version:t.version}:{}};return Pe(e,n)}validate(e,t){this._ensureLive(),e=this._normalizeHelm(e);let{mol:n,diagnostics:o}=this.parse(e,{mode:\"lenient\"}),r=t?.mode!==void 0?{mode:t.mode}:{},s=wn(n,this.monomerLib,r);return [...o,...s]}canonicalize(e){this._ensureLive(),e=this._normalizeHelm(e);let{mol:t}=this.parse(e,{mode:\"lenient\"}),n=vn(t);return Pe(n,{canonicalize:true,version:\"V2.0\"})}removeGaps(e){return this._ensureLive(),xn(this._normalizeHelm(e),this.monomerLib)}renderToSvg(e,t){this._ensureLive(),e=this._normalizeHelm(e);let n=this._resolveRenderOptions(t),o=this._renderKey(e,n),r=this._renderCache.get(o);if(r!==void 0)return this._renderHits+=1,r;this._renderMisses+=1;let{mol:s}=this.parse(e,{mode:\"lenient\"}),a=this._layout(s,n.bondLength),{svg:d}=Ht(a,n);return this._renderCache.set(o,d),d}renderMol(e,t){this._ensureLive();let n=this._resolveRenderOptions(t),{svg:o}=Ht(e,n);return o}renderMolResult(e,t){this._ensureLive();let n=this._resolveRenderOptions(t);return Ht(e,n)}async renderToPng(e,t){if(this._ensureLive(),e=this._normalizeHelm(e),typeof globalThis.OffscreenCanvas!=\"function\")throw new j(\"png-rendering-requires-browser\",\"HelmService.renderToPng requires OffscreenCanvas (browser-only).\");let n=this._resolveRenderOptions(t),{mol:o}=this.parse(e,{mode:\"lenient\"}),r=this._layout(o,n.bondLength);return di(r,n)}renderToCanvas(e,t,n,o){this._ensureLive(),t=this._normalizeHelm(t);let r=this._resolveRenderOptions(o),{mol:s}=this.parse(t,{mode:\"lenient\"}),a=this._layout(s,r.bondLength),{bbox:d,drawBox:l}=$t(e,a,n,r);return {mol:a,bbox:d,drawBox:l}}renderMolToCanvas(e,t,n,o){this._ensureLive();let r=this._resolveRenderOptions(o),{bbox:s,drawBox:a}=$t(e,t,n,r);return {mol:t,bbox:s,drawBox:a}}*renderMany(e,t){for(let n of e??[]){let o=this.renderToSvg(n.helm,t);yield {id:n.id,svg:o};}}getFormula(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return fe(t)}getMolWeight(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return De(t)}getExtinctionCoefficient(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return Oe(t)}getMolfile(e){this._ensureLive();let{mol:t}=this.parse(this._normalizeHelm(e),{mode:\"lenient\"});return Dt(t)}hasAtomicMolfileProvider(){return typeof this.options.atomicMolfileProvider==\"function\"}async getAtomicMolfile(e){this._ensureLive(),e=this._normalizeHelm(e);let t=this.options.atomicMolfileProvider;if(typeof t!=\"function\")throw new j(\"atomic-molfile-not-configured\",\"Set HelmServiceOptions.atomicMolfileProvider to enable atomic-level expansion.\");return await t(e,this.monomerLib)}hasExtraPanes(){let e=this.options.extraPanes;return e!==void 0&&e.size>0}getExtraPanes(){return this.options.extraPanes??ya}invalidate(e){if(e===void 0){this.clearCaches();return}for(let t of [this._parseCache,this._layoutCache,this._renderCache]){let n=[];for(let o of t.keys())e(o)&&n.push(o);for(let o of n)t.delete(o);}}clearCaches(){this._parseCache.clear(),this._layoutCache.clear(),this._renderCache.clear(),this._parseHits=0,this._parseMisses=0,this._layoutHits=0,this._layoutMisses=0,this._renderHits=0,this._renderMisses=0;}destroy(){this._destroyed||(this._destroyed=true,this._libUnsub(),this.clearCaches());}_ensureLive(){if(this._destroyed)throw new j(\"service-destroyed\",\"HelmService instance has been destroyed.\")}_normalizeHelm(e){return e==null?\"\":typeof e==\"string\"?e:String(e)}_resolveRenderOptions(e){let t={},n=e?.theme??this.theme;return t.theme=n,e?.width!==void 0&&(t.width=e.width),e?.height!==void 0&&(t.height=e.height),e?.backColor!==void 0&&(t.backColor=e.backColor),e?.padding!==void 0&&(t.padding=e.padding),e?.showIds!==void 0&&(t.showIds=e.showIds),e?.showAnnotations!==void 0&&(t.showAnnotations=e.showAnnotations),e?.bondLength!==void 0&&(t.bondLength=e.bondLength),e?.fontSize!==void 0&&(t.fontSize=e.fontSize),e?.maxScale!==void 0&&(t.maxScale=e.maxScale),e?.showRGroupLabels!==void 0&&(t.showRGroupLabels=e.showRGroupLabels),e?.selectedAtomIds!==void 0&&(t.selectedAtomIds=e.selectedAtomIds),e?.highlightedAtomIds!==void 0&&(t.highlightedAtomIds=e.highlightedAtomIds),e?.fixedModelBbox!==void 0&&(t.fixedModelBbox=e.fixedModelBbox),t}_renderKey(e,t){let o=(t.theme??this.theme).name,r=this._libCacheTag(),s=t.width??0,a=t.height??0,d=t.padding??-1,l=t.bondLength??-1,u=t.backColor??\"\",c=t.showIds===true?1:0,m=t.showAnnotations===false?0:1,p=t.maxScale??1;return `${r}|${o}|${s}x${a}|p${d}|b${l}|bg${u}|i${c}a${m}|s${p}|${e}`}_layout(e,t){let n=_a(e),o=`${this._libCacheTag()}|${t??\"d\"}|${n}`,r=this._layoutCache.get(o);if(r!==void 0)return this._layoutHits+=1,r;this._layoutMisses+=1;let s=t!==void 0?oe(e,{bondLength:t}):oe(e);return this._layoutCache.set(o,s),s}get stats(){return {parseHits:this._parseHits,parseMisses:this._parseMisses,layoutHits:this._layoutHits,layoutMisses:this._layoutMisses,renderHits:this._renderHits,renderMisses:this._renderMisses}}_libCacheTag(){let e=this.monomerLib,t=typeof e.version==\"number\"?e.version:0;return `${this.monomerLib.source}@${t}`}};var Q=class{constructor(e,t){this.atoms=e,this.bonds=t,this.isEmpty=e.size===0&&t.size===0,Object.freeze(this);}},fi=new Q(new Set,new Set),V={empty(){return fi},fromAtoms(i){return new Q(new Set(i),new Set)},fromBonds(i){return new Q(new Set,new Set(i))},fromAtomsAndBonds(i,e){return new Q(new Set(i),new Set(e))},union(...i){if(i.length===0)return fi;let e=new Set,t=new Set;for(let n of i){for(let o of n.atoms)e.add(o);for(let o of n.bonds)t.add(o);}return new Q(e,t)},difference(i,e){let t=new Set,n=new Set;for(let o of i.atoms)e.atoms.has(o)||t.add(o);for(let o of i.bonds)e.bonds.has(o)||n.add(o);return new Q(t,n)},intersect(i,e){let t=new Set,n=new Set;for(let o of i.atoms)e.atoms.has(o)&&t.add(o);for(let o of i.bonds)e.bonds.has(o)&&n.add(o);return new Q(t,n)},toggle(i,e){if(e.kind===\"atom\"){let n=new Set(i.atoms);return n.has(e.id)?n.delete(e.id):n.add(e.id),new Q(n,new Set(i.bonds))}let t=new Set(i.bonds);return t.has(e.id)?t.delete(e.id):t.add(e.id),new Q(new Set(i.atoms),t)},hasAtom(i,e){return i.atoms.has(e)},hasBond(i,e){return i.bonds.has(e)},equals(i,e){if(i===e)return  true;if(i.atoms.size!==e.atoms.size||i.bonds.size!==e.bonds.size)return  false;for(let t of i.atoms)if(!e.atoms.has(t))return  false;for(let t of i.bonds)if(!e.bonds.has(t))return  false;return  true}};function be(i){let e=i.monomer;return e===null?0:e.rgroups.length}function bi(i,e){let t=new Set;for(let r of e)r.a1.id===i.id&&r.r1.kind===\"numeric\"&&t.add(r.r1.r),r.a2.id===i.id&&r.r2.kind===\"numeric\"&&t.add(r.r2.r);let n=[],o=Array.from(t).sort((r,s)=>r-s);for(let r of o)n.push(r);return n}function W(i,e){let t=be(i);if(t===0)return [];let n=new Set(bi(i,e)),o=[];for(let r=1;r<=t;r++)n.has(r)||o.push(r);return o}function xa(i,e){return W(i,e).length>0}function Ot(i,e){let t=[];for(let n of e)if(n.a1.id===i.id){let o=n.r1.kind===\"numeric\"?n.r1.r:0;t.push({bond:n,side:\"r1\",rNumber:o});}else if(n.a2.id===i.id){let o=n.r2.kind===\"numeric\"?n.r2.r:0;t.push({bond:n,side:\"r2\",rNumber:o});}return t}function wa(i){switch(i){case g.AA:return x.PEPTIDE;case g.SUGAR:case g.BASE:case g.LINKER:case g.NUCLEOTIDE:return x.RNA;case g.CHEM:return x.CHEM;case g.BLOB:return x.BLOB}}function ka(i){switch(i){case x.PEPTIDE:return \"PEPTIDE\";case x.RNA:return \"RNA\";case x.CHEM:return \"CHEM\";case x.BLOB:return \"BLOB\";case x.G:return \"G\"}}function Aa(i){let e=0;for(let t of i.atoms)t.id>e&&(e=t.id);for(let t of i.bonds)t.id>e&&(e=t.id);return e}function Nt(i,e){return i.kind!==e.kind?false:i.kind===\"numeric\"&&e.kind===\"numeric\"?i.r===e.r:i.kind===\"positional\"&&e.kind===\"positional\"?i.position===e.position&&i.r===e.r:true}var N=class{constructor(e){this._atoms=new Map;this._atomOrder=[];this._bonds=new Map;this._bondOrder=[];this._chains=new Map;this._chainOrder=[];this._addedAtoms=new Set;this._removedAtoms=new Set;this._modifiedAtoms=new Set;this._addedBonds=new Set;this._removedBonds=new Set;this._modifiedBonds=new Set;this._topologyDirty=false;this._idgen=new ve;let t=Aa(e);for(let n=0;n<t;n++)this._idgen.next();for(let n of e.chains)this._chains.set(n.id,{id:n.id,polymerType:n.polymerType,backboneAtomIds:n.backboneAtoms.map(o=>o.id),bondIds:n.bonds.map(o=>o.id),annotation:n.annotation}),this._chainOrder.push(n.id);for(let n of e.atoms)this._atoms.set(n.id,{id:n.id,p:{x:n.p.x,y:n.p.y},biotype:n.biotype,symbol:n.symbol,monomer:n.monomer,bio:{...n.bio},hidden:n.hidden,selected:n.selected,highlighted:n.highlighted,tag:n.tag,branchAtomId:n.branchAtom?.id,inlineSource:n.inlineSource}),this._atomOrder.push(n.id);for(let n of e.bonds)this._bonds.set(n.id,{id:n.id,a1Id:n.a1.id,a2Id:n.a2.id,kind:n.kind,r1:n.r1,r2:n.r2,ratio:n.ratio,tag:n.tag}),this._bondOrder.push(n.id);this._groups=[...e.groups],this._annotations=e.annotations;}addAtom(e){let t=this._idgen.next(),n=wa(e.biotype),o=e.chainId??this._pickChainId(n),r=this._chains.get(o);r===void 0&&(r={id:o,polymerType:n,backboneAtomIds:[],bondIds:[],annotation:void 0},this._chains.set(o,r),this._chainOrder.push(o));let s=e.positionInChain??r.backboneAtomIds.length+1,a={id:t,p:{x:e.p.x,y:e.p.y},biotype:e.biotype,symbol:e.symbol,monomer:null,bio:{chainId:o,positionInChain:s,continuousId:0},hidden:false,selected:false,highlighted:false,tag:void 0,branchAtomId:void 0,inlineSource:void 0};this._atoms.set(t,a),this._atomOrder.push(t);let d=Math.max(0,Math.min(s-1,r.backboneAtomIds.length));return r.backboneAtomIds.splice(d,0,t),this._addedAtoms.add(t),this._topologyDirty=true,t}removeAtom(e){let t=this._atoms.get(e);if(t===void 0)return;let n=[];for(let s of this._bonds.values())(s.a1Id===e||s.a2Id===e)&&n.push(s.id);for(let s of n)this._removeBondInternal(s);for(let s of this._atoms.values())s.branchAtomId===e&&(s.branchAtomId=void 0);let o=this._chains.get(t.bio.chainId);if(o!==void 0){let s=o.backboneAtomIds.indexOf(e);s>=0&&o.backboneAtomIds.splice(s,1);}this._atoms.delete(e);let r=this._atomOrder.indexOf(e);r>=0&&this._atomOrder.splice(r,1),this._addedAtoms.has(e)?this._addedAtoms.delete(e):this._removedAtoms.add(e),this._modifiedAtoms.delete(e),this._topologyDirty=true;}updateAtom(e,t){let n=this._atoms.get(e);n!==void 0&&(t.p!==void 0&&(n.p={x:t.p.x,y:t.p.y}),t.symbol!==void 0&&(n.symbol=t.symbol),t.selected!==void 0&&(n.selected=t.selected),t.highlighted!==void 0&&(n.highlighted=t.highlighted),\"tag\"in t&&(n.tag=t.tag),t.hidden!==void 0&&(n.hidden=t.hidden),this._addedAtoms.has(e)||this._modifiedAtoms.add(e));}addBond(e){if(!this._atoms.has(e.a1))throw new Error(`Transaction.addBond: atom ${e.a1} does not exist`);if(!this._atoms.has(e.a2))throw new Error(`Transaction.addBond: atom ${e.a2} does not exist`);for(let r of this._bonds.values()){let s=r.a1Id===e.a1&&r.a2Id===e.a2&&Nt(r.r1,e.r1)&&Nt(r.r2,e.r2),a=r.a1Id===e.a2&&r.a2Id===e.a1&&Nt(r.r1,e.r2)&&Nt(r.r2,e.r1);if(s||a)throw new Error(`Transaction.addBond: duplicate bond ${e.a1}:${yi(e.r1)}-${e.a2}:${yi(e.r2)}`)}let t=this._idgen.next();this._bonds.set(t,{id:t,a1Id:e.a1,a2Id:e.a2,kind:e.kind,r1:e.r1,r2:e.r2,ratio:void 0,tag:void 0}),this._bondOrder.push(t);let n=this._atoms.get(e.a1),o=this._atoms.get(e.a2);if(n!==void 0&&o!==void 0&&n.bio.chainId===o.bio.chainId){let r=this._chains.get(n.bio.chainId);r!==void 0&&r.bondIds.push(t);}return this._addedBonds.add(t),this._topologyDirty=true,t}removeBond(e){this._bonds.has(e)&&(this._removeBondInternal(e),this._topologyDirty=true);}updateBond(e,t){let n=this._bonds.get(e);n!==void 0&&(\"tag\"in t&&(n.tag=t.tag),\"ratio\"in t&&(n.ratio=t.ratio),this._addedBonds.has(e)||this._modifiedBonds.add(e));}commit(){let e=new Map;for(let d of this._atomOrder){let l=this._atoms.get(d);if(l===void 0)continue;let u={id:l.id,p:{x:l.p.x,y:l.p.y},biotype:l.biotype,symbol:l.symbol,monomer:l.monomer,bio:{...l.bio},hidden:l.hidden,selected:l.selected,highlighted:l.highlighted,...l.tag!==void 0?{tag:l.tag}:{},...l.inlineSource!==void 0?{inlineSource:l.inlineSource}:{}};e.set(d,u);}for(let d of this._atomOrder){let l=this._atoms.get(d);if(l===void 0||l.branchAtomId===void 0)continue;let u=e.get(d),c=e.get(l.branchAtomId);u===void 0||c===void 0||(u.branchAtom=c);}let t=new Map;for(let d of this._bondOrder){let l=this._bonds.get(d);if(l===void 0)continue;let u=e.get(l.a1Id),c=e.get(l.a2Id);if(u===void 0||c===void 0)continue;let m={id:l.id,a1:u,a2:c,kind:l.kind,r1:l.r1,r2:l.r2,...l.ratio!==void 0?{ratio:{...l.ratio}}:{},...l.tag!==void 0?{tag:l.tag}:{}};t.set(d,m);}let n=[];for(let d of this._chainOrder){let l=this._chains.get(d);if(l===void 0||l.backboneAtomIds.length===0&&l.bondIds.length===0)continue;let u=[];for(let m of l.backboneAtomIds){let p=e.get(m);p!==void 0&&u.push(p);}let c=[];for(let m of l.bondIds){let p=t.get(m);p!==void 0&&c.push(p);}n.push({id:l.id,polymerType:l.polymerType,backboneAtoms:u,bonds:c,...l.annotation!==void 0?{annotation:l.annotation}:{}});}let o=this._atomOrder.map(d=>e.get(d)).filter(d=>d!==void 0),r=this._bondOrder.map(d=>t.get(d)).filter(d=>d!==void 0),s={atoms:o,bonds:r,chains:n,groups:[...this._groups],annotations:this._annotations};this._topologyDirty&&(s=Ma(s));let a=Object.freeze({addedAtomIds:new Set(this._addedAtoms),removedAtomIds:new Set(this._removedAtoms),addedBondIds:new Set(this._addedBonds),removedBondIds:new Set(this._removedBonds),modifiedAtomIds:new Set(this._modifiedAtoms),modifiedBondIds:new Set(this._modifiedBonds)});return this._addedAtoms.clear(),this._removedAtoms.clear(),this._modifiedAtoms.clear(),this._addedBonds.clear(),this._removedBonds.clear(),this._modifiedBonds.clear(),this._topologyDirty=false,{mol:s,changes:a}}_removeBondInternal(e){if(this._bonds.get(e)===void 0)return;this._bonds.delete(e);let n=this._bondOrder.indexOf(e);n>=0&&this._bondOrder.splice(n,1);for(let o of this._chains.values()){let r=o.bondIds.indexOf(e);r>=0&&o.bondIds.splice(r,1);}this._addedBonds.has(e)?this._addedBonds.delete(e):this._removedBonds.add(e),this._modifiedBonds.delete(e);}_pickChainId(e){let t=ka(e),n=1;for(;this._chains.has(`${t}${n}`);)n+=1;return `${t}${n}`}};function yi(i){switch(i.kind){case \"numeric\":return `R${i.r}`;case \"unspecified\":return \"?\";case \"wildcard\":return \"*\";case \"pair\":return \"pair\";case \"positional\":return `${i.position}pos:R${i.r}`}}function Ma(i){let e=Le(i),t=new Map;for(let a of i.atoms){let d=e.get(a.id);if(d===void 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o=[];for(let r of e.bonds)o.push({bond:r,a:r.a1.p,b:r.a2.p});this.atoms=n,this.bonds=o;}test(e){let t=null,n=null;for(let r of this.atoms){if(!Ft(e,r.bbox))continue;let s=e.x-r.atom.p.x,a=e.y-r.atom.p.y,d=Math.sqrt(s*s+a*a);d>r.hitRadius||(t===null||d<t.d?(n=t,t={entry:r,d}):(n===null||d<n.d)&&(n={entry:r,d}));}if(t!==null)return {atom:t.entry.atom};let o=null;for(let r of this.bonds){let s=Ta(e,r.a,r.b);s>this.bondHitWidth||(o===null||s<o.d)&&(o={entry:r,d:s});}return o!==null?{bond:o.entry.bond}:null}testRect(e){let t=[];for(let o of this.atoms)Ft(o.atom.p,e)&&t.push(o.atom);let n=[];for(let o of this.bonds)Ft(o.a,e)&&Ft(o.b,e)&&n.push(o.bond);return {atoms:t,bonds:n}}atomCount(){return this.atoms.length}bondCount(){return this.bonds.length}};function Ft(i,e){return i.x>=e.x&&i.x<=e.x+e.width&&i.y>=e.y&&i.y<=e.y+e.height}function Ta(i,e,t){let n=t.x-e.x,o=t.y-e.y,r=n*n+o*o;if(r===0){let c=i.x-e.x,m=i.y-e.y;return Math.sqrt(c*c+m*m)}let 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svgRoot(){return this._svgRoot}get width(){return this._width}get height(){return this._height}resize(e,t){this._destroyed||(this._width=e,this._height=t,this._renderFresh());}redraw(){this._destroyed||this._renderFresh();}destroy(){if(this._destroyed)return;this._destroyed=true;for(let t of this._unsubs)t();this._unsubs.length=0;let e=this.host.querySelector(\".hw-editor-view\");e!==null&&e.parentNode!==null&&e.parentNode.removeChild(e),U(this._tooltip),U(this._bondTooltip),this._tooltip=null,this._bondTooltip=null;}_renderFresh(){let e=this._editor.getService(),t=this._currentTheme(),n=this._editor.getMol();this._pinnedBbox===null&&(this._pinnedBbox=Dn(n,t));let o=e.renderMol(n,{width:this._width,height:this._height,theme:t,fixedModelBbox:this._pinnedBbox});this._svgRoot=vi(this.host,o);let r=this._svgRoot.querySelector(\".hw-content\");return this._baseTransform=r!==null?r.getAttribute(\"transform\")??\"\":\"\",this._svgRoot.setAttribute(\"data-testid\",\"editor-svg\"),this._applyOverlaysToCurrent(),(this._viewport.scale!==1||this._viewport.offset.x!==0||this._viewport.offset.y!==0)&&this._applyViewport(this._viewport),this._svgRoot}_refreshOverlays(e){this._applyOverlaysToCurrent();}_applyOverlaysToCurrent(){let e=this._editor.getMol(),t=this._editor.getSelection(),n=gi(e,{theme:this._currentTheme(),selectedAtomIds:t.atoms,highlightedAtomIds:this._editorHighlights()});this._spliceLayer(\"hw-highlights\",n.highlightLayer),this._spliceLayer(\"hw-selections\",n.selectionLayer);}_spliceLayer(e,t){let n=this._svgRoot.querySelector(`.${e}`);if(n===null||n.parentNode===null)return;let o=this._doc.createElementNS(\"http://www.w3.org/2000/svg\",\"svg\");o.innerHTML=t;let r=o.querySelector(`.${e}`);r!==null&&n.parentNode.replaceChild(r,n);}_editorHighlights(){let e=this._editor;return typeof e._currentHighlights==\"function\"?e._currentHighlights():new Set}_currentTheme(){let e=this._editor;return typeof e._currentTheme==\"function\"?e._currentTheme():this._editor.getService().theme}_applyResize(e,t){this._width=e,this._height=t,this._pinnedBbox=null,this._renderFresh();}_applyViewport(e){let n=this._svgRoot.querySelector(\".hw-content\");if(n===null)return;let o=`translate(${e.offset.x} ${e.offset.y}) scale(${e.scale})`,r=this._baseTransform===\"\"?o:`${o} ${this._baseTransform}`;n.setAttribute(\"transform\",r);}_showTooltip(e,t,n){let o=this._tooltip;if(o===null)return;let r=e.symbol===\"\"?\"?\":e.symbol,s=e.monomer?.name??\"\",a=e.bio.positionInChain,d=e.bio.chainId===\"\"?\"?\":e.bio.chainId,l=s!==\"\"&&s!==r?`${s} @ ${d}:${a}`:`${r} @ ${d}:${a}`,u=this._renderRdkitTooltipSvg(e);Te(this._doc,o,{symbol:r,name:l,rdkitSvg:u,rdkitTestid:\"atom-tooltip-rdkit-svg\"});let c=s!==\"\"&&s!==r?`${r} \\u2014 ${s}  @ ${d}:${a}`:`${r}  @ ${d}:${a}`,m=this._doc.createElement(\"div\");m.setAttribute(\"class\",\"hw-atom-tooltip__text\"),m.style.display=\"none\",m.appendChild(this._doc.createTextNode(c)),o.appendChild(m),Y(o,t,n);}_renderRdkitTooltipSvg(e){let n=this._editor.getService().options.rdkitModule;if(n==null)return null;let o=e.monomer;if(o===null)return null;let r=o.smiles;if(r===void 0||r===\"\")return null;let s=`${o.polymerType}:${o.symbol}`;if(this._rdkitSvgCache.has(s))return this._rdkitSvgCache.get(s)??null;let a=ye(n,r,220,140);if(this._rdkitSvgCache.size>=Ut._RDKIT_CACHE_LIMIT){let d=this._rdkitSvgCache.keys().next().value;d!==void 0&&this._rdkitSvgCache.delete(d);}return this._rdkitSvgCache.set(s,a),a}_hideTooltip(){U(this._tooltip);}_showBondTooltip(e,t,n){let o=this._bondTooltip;if(o===null)return;let r=wi(e.r1),s=wi(e.r2),a=`${e.a1.symbol}@${e.a1.bio.chainId}:${e.a1.bio.positionInChain}`,d=`${e.a2.symbol}@${e.a2.bio.chainId}:${e.a2.bio.positionInChain}`;Te(this._doc,o,{symbol:`${r}-${s} (${e.kind})`,name:`${a} \\u2194 ${d}`}),Y(o,t,n);}_hideBondTooltip(){U(this._bondTooltip);}_paintBondPreview(e,t,n){let o=\"http://www.w3.org/2000/svg\",r=this._svgRoot.querySelector(\".hw-content\");if(r===null)return;let s=r.querySelector(\".hw-bond-preview\");s===null&&(s=this._doc.createElementNS(o,\"line\"),s.setAttribute(\"class\",\"hw-bond-preview\"),s.setAttribute(\"data-testid\",\"bond-preview\"),s.setAttribute(\"stroke-dasharray\",\"6 4\"),s.setAttribute(\"stroke-width\",\"2\"),s.setAttribute(\"fill\",\"none\"),s.setAttribute(\"pointer-events\",\"none\"),r.appendChild(s)),s.setAttribute(\"x1\",String(e.x)),s.setAttribute(\"y1\",String(e.y)),s.setAttribute(\"x2\",String(t.x)),s.setAttribute(\"y2\",String(t.y)),s.setAttribute(\"stroke\",n?\"#1f5fcd\":\"#999999\");}_clearBondPreview(){let e=this._svgRoot.querySelector(\".hw-bond-preview\");e!==null&&e.parentNode!==null&&e.parentNode.removeChild(e);}_paintSelectionRect(e,t){let n=Math.min(e.x,t.x),o=Math.min(e.y,t.y),r=Math.abs(e.x-t.x),s=Math.abs(e.y-t.y);this._paintSelectionRectAt(n,o,r,s);}_paintSelectionRectFromRect(e){this._paintSelectionRectAt(e.x,e.y,e.width,e.height);}_paintSelectionRectAt(e,t,n,o){let r=\"http://www.w3.org/2000/svg\",s=this._svgRoot.querySelector(\".hw-content\");if(s===null)return;let a=s.querySelector(\".hw-selection-rect\");a===null&&(a=this._doc.createElementNS(r,\"rect\"),a.setAttribute(\"class\",\"hw-selection-rect\"),a.setAttribute(\"data-testid\",\"selection-rect\"),a.setAttribute(\"fill\",\"rgba(31, 95, 205, 0.08)\"),a.setAttribute(\"stroke\",\"#1f5fcd\"),a.setAttribute(\"stroke-width\",\"1\"),a.setAttribute(\"stroke-dasharray\",\"4 3\"),a.setAttribute(\"pointer-events\",\"none\"),s.appendChild(a)),a.setAttribute(\"x\",String(e)),a.setAttribute(\"y\",String(t)),a.setAttribute(\"width\",String(n)),a.setAttribute(\"height\",String(o));}_clearSelectionRect(){let e=this._svgRoot.querySelector(\".hw-selection-rect\");e!==null&&e.parentNode!==null&&e.parentNode.removeChild(e);}};Ut._RDKIT_CACHE_LIMIT=256;var Vt=Ut;function wi(i){switch(i.kind){case \"numeric\":return `R${i.r}`;case \"unspecified\":return \"?\";case \"wildcard\":return \"*\";case \"pair\":return \"pair\";case \"positional\":return `${i.position}pos:R${i.r}`}}var re=class re{constructor(e,t){this._onClose=null;this._primaryAction=null;this._host=e,this._doc=t.documentImpl??S(e);let n=this._doc,o={class:\"hw-modal-backdrop\",role:\"presentation\"};t.testId!==void 0&&(o[\"data-testid\"]=`dialog-${t.testId}`);let r=v(n,\"div\",o),s={class:\"hw-modal\",role:\"dialog\",\"aria-modal\":\"true\",\"aria-label\":t.title};t.testId!==void 0&&(s[\"data-testid\"]=`dialog-${t.testId}-frame`);let a=v(n,\"div\",s),d=v(n,\"div\",{class:\"hw-modal__header\"},[t.title]),l=v(n,\"div\",{class:\"hw-modal__body\"});a.appendChild(d),a.appendChild(l),r.appendChild(a);let u=c=>{c.stopPropagation();};for(let c of [\"mousedown\",\"mousemove\",\"mouseup\",\"mouseover\",\"mouseenter\",\"mouseleave\",\"wheel\",\"contextmenu\",\"dblclick\",\"keydown\",\"keyup\",\"keypress\"])r.addEventListener(c,u);a.addEventListener(\"keydown\",c=>{let m=c;if(m.key!==\"Enter\"||m.target?.tagName===\"TEXTAREA\")return;let p=this._primaryAction;p!==null&&(m.preventDefault?.(),m.stopImmediatePropagation?.(),p());}),r.addEventListener(\"click\",c=>{if(c.target===r){this.close();return}c.stopPropagation();}),this.root=r,this.body=l;}static anyOpen(){return re._openStack.length>0}static closeTopmost(){let e=re._openStack[re._openStack.length-1];return e===void 0?false:(e.close(),true)}open(e){this._onClose=e??null,this.root.parentNode===null&&this._host.appendChild(this.root),re._openStack.includes(this)||re._openStack.push(this),Gt(this._doc);}close(){let e=re._openStack.indexOf(this);e>=0&&re._openStack.splice(e,1),this.root.parentNode!==null&&this.root.parentNode.removeChild(this.root);let t=this._onClose;this._onClose=null,t!==null&&t();}setPrimaryAction(e){this._primaryAction=e;}get isOpen(){return this.root.parentNode!==null}};re._openStack=[];var X=re;function Ve(i,e,t,n){let o=`hw-input-${Math.random().toString(36).slice(2,9)}`,r=v(i,\"label\",{for:o,class:\"hw-modal__label\"},[e]),s=i.createElement(\"input\");return s.setAttribute(\"id\",o),s.setAttribute(\"type\",\"text\"),s.setAttribute(\"class\",\"hw-modal__input\"),n!==void 0&&s.setAttribute(\"data-testid\",n),s.value=t,{row:v(i,\"div\",{class:\"hw-modal__row\"},[r,s]),input:s}}function Ue(i,e,t,n,o){let r=`hw-sel-${Math.random().toString(36).slice(2,9)}`,s=v(i,\"label\",{for:r,class:\"hw-modal__label\"},[e]),a=i.createElement(\"select\");a.setAttribute(\"id\",r),a.setAttribute(\"class\",\"hw-modal__select\"),o!==void 0&&a.setAttribute(\"data-testid\",o);for(let l of t){let u=i.createElement(\"option\");u.setAttribute(\"value\",l.value),l.value===n&&u.setAttribute(\"selected\",\"\"),u.appendChild(i.createTextNode(l.label)),a.appendChild(u);}return {row:v(i,\"div\",{class:\"hw-modal__row\"},[s,a]),select:a}}function ze(i,e){let t=i.createElement(\"button\");t.setAttribute(\"class\",\"hw-modal__ok\"),t.setAttribute(\"type\",\"button\"),e!==void 0&&t.setAttribute(\"data-testid\",`${e}-ok`),t.appendChild(i.createTextNode(\"OK\"));let n=i.createElement(\"button\");return n.setAttribute(\"class\",\"hw-modal__cancel\"),n.setAttribute(\"type\",\"button\"),e!==void 0&&n.setAttribute(\"data-testid\",`${e}-cancel`),n.appendChild(i.createTextNode(\"Cancel\")),{row:v(i,\"div\",{class:\"hw-modal__actions\"},[t,n]),ok:t,cancel:n}}var Ke=class{constructor(e,t){this._modal=null;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"ChooseRDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}open(e,t,n){this.close();let o=this._editor._getHost();if(o===null)return Promise.resolve(null);let r=new X(o,{documentImpl:this._doc,title:\"Choose R-Groups\",testId:\"choose-r\"});this._modal=r;let s=Ai(e,n?.freeR1,n?.currentR1,this._editor),a=Ai(t,n?.freeR2,n?.currentR2,this._editor),d=v(this._doc,\"div\",{class:\"hw-modal__info\"},[`${e.symbol} (${e.bio.chainId})`]),l=n?.currentR1!==void 0?String(n.currentR1):s[0]?.value??\"1\",u=n?.currentR2!==void 0?String(n.currentR2):a[0]?.value??\"1\",c=Ue(this._doc,\"R-group on side A\",s,l,\"choose-r-r1\"),m=v(this._doc,\"div\",{class:\"hw-modal__info\"},[`${t.symbol} (${t.bio.chainId})`]),p=Ue(this._doc,\"R-group on side B\",a,u,\"choose-r-r2\"),h=ze(this._doc,\"choose-r\"),y=[];return s.length===0&&y.push(v(this._doc,\"div\",{class:\"hw-modal__info hw-modal__note-fully-booked\"},[`All R-groups on ${e.symbol} are in use.`])),a.length===0&&y.push(v(this._doc,\"div\",{class:\"hw-modal__info hw-modal__note-fully-booked\"},[`All R-groups on ${t.symbol} are in use.`])),new Promise(f=>{let _=false,b=k=>{_||(_=true,f(k));},A=k=>{b(k),this.close();},w=()=>A({r1:ki(c.select),r2:ki(p.select)});h.ok.addEventListener(\"click\",w),h.cancel.addEventListener(\"click\",()=>A(null)),r.setPrimaryAction(w),r.body.appendChild(d),r.body.appendChild(c.row),r.body.appendChild(m),r.body.appendChild(p.row);for(let k of y)r.body.appendChild(k);r.body.appendChild(h.row),r.open(()=>b(null));})}get isOpen(){return this._modal!==null&&this._modal.isOpen}close(){this._modal!==null&&(this._modal.close(),this._modal=null);}};function ki(i){let e=i.value;if(typeof e==\"string\"&&e.length>0){let o=Number(e);if(Number.isFinite(o)&&o>=1)return o}let t=i.querySelectorAll(\"option\");for(let o of Array.from(t))if(o.getAttribute(\"selected\")!==null){let r=o.getAttribute(\"value\")??\"\",s=Number(r);if(Number.isFinite(s)&&s>=1)return s}let n=t[0];if(n!==void 0){let o=n.getAttribute(\"value\")??\"\",r=Number(o);if(Number.isFinite(r)&&r>=1)return r}return 1}function Ai(i,e,t,n){let o=i.monomer?.rgroups;if(o===void 0||o.length===0)return [{value:\"1\",label:\"R1\"},{value:\"2\",label:\"R2\"},{value:\"3\",label:\"R3\"}];let r;if(e!==void 0)r=new Set(e);else if(r=new Set(W(i,n.getMol().bonds)),r.size===0)for(let d=1;d<=o.length;d++)r.add(d);t!==void 0&&t>=1&&t<=o.length&&r.add(t);let s=[],a=Array.from(r).sort((d,l)=>d-l);for(let d of a){let l=o[d-1];if(l===void 0)continue;let u=l.capGroupName!==void 0&&l.capGroupName!==\"\"?` (${l.capGroupName})`:\"\";s.push({value:String(d),label:`${l.label}${u}`});}return s}var Mi=\"next-add-cursor\",rt=28,zt=rt*2;function Ti(i){let e=\"data-testid\";for(let n=0;n<i.body.children.length;n++){let o=i.body.children[n];if(o!==void 0&&o.getAttribute(e)===Mi)return o}let t=i.createElement(\"div\");return t.className=\"hw-next-add-cursor\",t.setAttribute(e,Mi),t.style.display=\"none\",i.body.appendChild(t),t}function Si(i,e,t,n,o,r,s){let d=$e({p:{x:0,y:0},biotype:t,symbol:e},o),u=D(n,t,o.colorTheme).background,c=kt(u),m=e.length,p=m<=1?1:Math.min(1,2/m),h=o.fontSize*p,y=`<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"${-rt} ${-rt} ${zt} ${zt}\" width=\"${zt}\" height=\"${zt}\" class=\"hw-next-add-cursor__svg\" aria-hidden=\"true\"><path d=\"${d}\" fill=\"${u}\" stroke=\"${u}\" stroke-width=\"5\" stroke-linejoin=\"round\" stroke-linecap=\"round\"/><text x=\"0\" y=\"0\" text-anchor=\"middle\" dominant-baseline=\"central\" font-family=\"Helvetica Neue, Helvetica, Arial, sans-serif\" font-size=\"${h}\" fill=\"${c}\">${Sa(e)}</text></svg>`;i.innerHTML=y;let f=i.style;f.left=`${r-rt}px`,f.top=`${s-rt}px`,f.display=\"block\";}function st(i){i!==null&&(i.style.display=\"none\");}function Sa(i){let e=\"\";for(let t=0;t<i.length;t++){let n=i.charAt(t);n===\"<\"?e+=\"&lt;\":n===\">\"?e+=\"&gt;\":n===\"&\"?e+=\"&amp;\":e+=n;}return e}var Kt=class{constructor(e,t,n){this._hoverAtom=null;this._hoverBond=null;this._dragOrigin=null;this._bondStart=null;this._bondDragMoved=false;this._rectDragHappened=false;this._chooseRDialog=null;this._panStart=null;this._atomDragState=null;this._panMoved=false;this._atomDragMoved=false;this._nextAddCursorEl=null;this._destroyed=false;this._unsubs=[];this._host=e,this._editor=t,this._enableContextMenu=n?.enableContextMenu??true,this._tester=new q(t.getMol(),t._currentTheme()),this._unsubs.push(t.on(\"mol:changed\",()=>{this._tester=new q(this._editor.getMol(),this._editor._currentTheme()),this._hoverAtom=null,this._hoverBond=null;})),this._unsubs.push(t.on(\"option:change\",o=>{(o.key===\"mode\"||o.key===\"nextAdd\")&&st(this._nextAddCursorEl);})),this._onMove=o=>this._handleMove(o),this._onClick=o=>this._handleClick(o),this._onDblClick=o=>this._handleDblClick(o),this._onContextMenu=o=>this._handleContextMenu(o),this._onMouseDown=o=>this._handleMouseDown(o),this._onMouseUp=o=>this._handleMouseUp(o),this._onMouseLeave=o=>this._handleMouseLeave(o),this._onWheel=o=>this._handleWheel(o),e.addEventListener(\"mousemove\",this._onMove),e.addEventListener(\"click\",this._onClick),e.addEventListener(\"dblclick\",this._onDblClick),e.addEventListener(\"contextmenu\",this._onContextMenu),e.addEventListener(\"mousedown\",this._onMouseDown),e.addEventListener(\"mouseup\",this._onMouseUp),e.addEventListener(\"mouseleave\",this._onMouseLeave),e.addEventListener(\"wheel\",this._onWheel,{passive:false});}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this._host.removeEventListener(\"mousemove\",this._onMove),this._host.removeEventListener(\"click\",this._onClick),this._host.removeEventListener(\"dblclick\",this._onDblClick),this._host.removeEventListener(\"contextmenu\",this._onContextMenu),this._host.removeEventListener(\"mousedown\",this._onMouseDown),this._host.removeEventListener(\"mouseup\",this._onMouseUp),this._host.removeEventListener(\"mouseleave\",this._onMouseLeave),this._host.removeEventListener(\"wheel\",this._onWheel),this._chooseRDialog!==null&&(this._chooseRDialog.close(),this._chooseRDialog=null),st(this._nextAddCursorEl),this._nextAddCursorEl=null;}}_handleMove(e){if(this._panStart!==null){let s=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),a=s.x-this._panStart.origin.x,d=s.y-this._panStart.origin.y;this._editor.panTo({x:this._panStart.initialOffset.x+a,y:this._panStart.initialOffset.y+d}),this._panMoved=true;return}if(this._atomDragState!==null){let s=this._toModel(e),a=s.x-this._atomDragState.pointerDownModel.x,d=s.y-this._atomDragState.pointerDownModel.y,l=[];for(let u of this._atomDragState.atomIds){let c=this._atomDragState.initialPositions.get(u);c!==void 0&&l.push({atomId:u,p:{x:c.x+a,y:c.y+d}});}this._editor.moveAtoms(l),this._atomDragMoved=true;return}let t=this._toModel(e),n=this._tester.test(t),o=n?.atom??null,r=n?.bond??null;if(this._bondStart!==null){this._bondDragMoved=true;let s=o!==null&&o.id!==this._bondStart.id?o:null;this._editor.fire(\"bond:preview\",{start:this._bondStart,cursor:t,candidate:s,kind:this._editor.getMode()===\"hbond\"?\"hbond\":\"backbone\"});}if(this._hoverAtom!==null&&(o===null||o.id!==this._hoverAtom.id)&&(this._editor.fire(\"monomer:hover-end\",{atom:this._hoverAtom}),this._hoverAtom=null),o!==null&&(this._hoverAtom===null||this._hoverAtom.id!==o.id)&&(this._hoverAtom=o,this._editor.fire(\"monomer:hover\",{atom:o,clientX:e.clientX,clientY:e.clientY,modelX:t.x,modelY:t.y})),this._hoverBond!==null&&(r===null||r.id!==this._hoverBond.id)&&(this._editor.fire(\"bond:hover-end\",{bond:this._hoverBond}),this._hoverBond=null),r!==null&&(this._hoverBond===null||this._hoverBond.id!==r.id)&&(this._hoverBond=r,this._editor.fire(\"bond:hover\",{bond:r,clientX:e.clientX,clientY:e.clientY})),this._dragOrigin!==null){let s=Ri(this._dragOrigin,t);this._editor.fire(\"selection:rectangle-update\",{rect:s});}this._updateNextAddCursor(e);}_handleClick(e){if(this._bondDragMoved){this._bondDragMoved=false;return}if(this._rectDragHappened){this._rectDragHappened=false;return}if(this._panMoved){this._panMoved=false;return}if(this._atomDragMoved){this._atomDragMoved=false;return}let t=this._toModel(e),n=this._tester.test(t),o=Bi(e),r=this._editor.getMode();if(r===\"eraser\"){if(n?.atom!==void 0){this._editor.removeAtom(n.atom);return}if(n?.bond!==void 0){this._editor.removeBond(n.bond);return}return}if(n?.atom!==void 0){if(r===\"select\"&&!o.ctrl&&!o.shift&&!o.meta){let s=this._editor.getNextAddSymbol();if(s!==null){if(n.atom.biotype===s.biotype){this._editor.replaceMonomer(n.atom,s.symbol);return}this._editor.fire(\"editor:status\",{message:`Cannot replace: ${n.atom.biotype} is incompatible with ${s.biotype}`,severity:\"warn\",durationMs:3e3});return}}this._editor.fire(\"monomer:click\",{atom:n.atom,modifiers:o,clientX:e.clientX,clientY:e.clientY});return}if(n?.bond!==void 0){this._editor.fire(\"bond:click\",{bond:n.bond,modifiers:o});return}if(this._addsEnabled()){let s=this._editor.getNextAddSymbol();if(s!==null){this._editor.addAtom(t,s.biotype,s.symbol);return}}!o.shift&&!o.ctrl&&!o.meta&&this._editor.clearSelection();}_handleDblClick(e){let t=this._toModel(e),n=this._tester.test(t),o=Bi(e);if(n?.atom!==void 0){this._editor.fire(\"monomer:dblclick\",{atom:n.atom,modifiers:o});return}n===null&&this._editor.fitToContent();}_handleContextMenu(e){this._enableContextMenu||e.preventDefault();let t=this._toModel(e),n=this._tester.test(t),r=()=>{e.preventDefault();};n?.atom!==void 0?this._editor.fire(\"monomer:contextmenu\",{atom:n.atom,clientX:e.clientX,clientY:e.clientY,preventDefault:r}):n?.bond!==void 0&&this._editor.fire(\"bond:contextmenu\",{bond:n.bond,clientX:e.clientX,clientY:e.clientY,preventDefault:r});}_handleMouseDown(e){if(e.button!==0)return;let t=this._toModel(e),n=this._tester.test(t),o=this._editor.getMode(),r=e.ctrlKey===true||e.metaKey===true,s=e.shiftKey===true;if(n?.atom!==void 0){if(o===\"move\"||o===\"select\"&&r){let a=this._editor.getSelection(),l=a.atoms.has(n.atom.id)?Array.from(a.atoms):[n.atom.id],u=this._editor.getMol(),c=new Map;for(let m of l){let p=u.atoms.find(h=>h.id===m);p!==void 0&&c.set(m,{x:p.p.x,y:p.p.y});}this._atomDragState={atomIds:l,pointerDownModel:{x:t.x,y:t.y},initialPositions:c},this._atomDragMoved=false;return}this._bondStart=n.atom,this._bondDragMoved=false;return}if(n===null){if(o===\"move\"||o===\"select\"&&!s){let a=this._editor.getViewport();this._panStart={origin:this._toViewBox({clientX:e.clientX,clientY:e.clientY}),initialOffset:{x:a.offset.x,y:a.offset.y}},this._panMoved=false;return}o===\"select\"&&s&&(this._dragOrigin=t,this._editor.fire(\"selection:rectangle-start\",{origin:t}));}}_handleMouseUp(e){if(this._panStart!==null){this._panStart=null;return}if(this._atomDragState!==null){this._atomDragState=null;return}if(this._bondStart!==null){let a=this._bondStart,d=this._bondDragMoved;this._bondStart=null;let l=this._toModel(e),c=this._tester.test(l)?.atom;if(d&&c!==void 0&&c.id!==a.id){if(this._editor.fire(\"bond:preview-end\",{start:a}),this._editor.getMode()===\"hbond\"){try{this._editor.addHydrogenBond(a,c);}catch{this._editor.fire(\"bond:cancel\",{start:a});}return}let m=a.bio.chainId===c.bio.chainId&&Li(a,c,this._editor.getMol())?\"backbone\":\"cross-polymer\",p=Ei(a,c,this._editor.getMol().bonds,m);if(p.mode===\"fail\"){this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"editor:status\",{message:p.reason,severity:\"error\",durationMs:3e3});return}if(p.mode===\"auto\"){try{this._editor.addBond(a,c,p.r1,p.r2,p.kind);}catch{this._editor.fire(\"bond:cancel\",{start:a});}return}this._openChooseR(a,c,m,p.freeR1,p.freeR2);return}if(d){let m=this._addsEnabled()?this._editor.getNextAddSymbol():null;if(m!==null){let p;try{p=this._editor.addAtom(l,m.biotype,m.symbol);}catch{this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"bond:preview-end\",{start:a});return}let h=this._editor.getMol().atoms.find(A=>A.id===a.id);if(h===void 0){this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"bond:preview-end\",{start:a});return}let y=h.bio.chainId===p.bio.chainId&&Li(h,p,this._editor.getMol())?\"backbone\":\"cross-polymer\",f=W(h,this._editor.getMol().bonds),_=W(p,this._editor.getMol().bonds);if(f.includes(2)&&_.includes(1)){try{this._editor.addBond(h,p,2,1,y);}catch{this._editor.fire(\"bond:cancel\",{start:a});}this._editor.fire(\"bond:preview-end\",{start:a});return}let b=Ei(h,p,this._editor.getMol().bonds,y);if(b.mode===\"fail\"){this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"editor:status\",{message:b.reason,severity:\"error\",durationMs:3e3}),this._editor.fire(\"bond:preview-end\",{start:a});return}if(b.mode===\"auto\"){try{this._editor.addBond(h,p,b.r1,b.r2,b.kind);}catch{this._editor.fire(\"bond:cancel\",{start:a});}this._editor.fire(\"bond:preview-end\",{start:a});return}this._editor.fire(\"bond:preview-end\",{start:a}),this._openChooseR(h,p,y,b.freeR1,b.freeR2);return}this._editor.fire(\"bond:cancel\",{start:a}),this._editor.fire(\"bond:preview-end\",{start:a});return}return}if(this._dragOrigin===null)return;let t=this._toModel(e),n=Ri(this._dragOrigin,t);this._dragOrigin=null;let o=this._tester.testRect(n),r=V.fromAtomsAndBonds(o.atoms.map(a=>a.id),o.bonds.map(a=>a.id)),s=V.union(this._editor.getSelection(),r);this._editor.setSelection(s),this._editor.fire(\"selection:rectangle-end\",{rect:n,selection:s}),this._rectDragHappened=true,s.atoms.size>0&&this._editor.getMode()===\"select\"&&this._editor.setMode(\"move\");}_handleMouseLeave(e){this._hoverAtom!==null&&(this._editor.fire(\"monomer:hover-end\",{atom:this._hoverAtom}),this._hoverAtom=null),this._hoverBond!==null&&(this._editor.fire(\"bond:hover-end\",{bond:this._hoverBond}),this._hoverBond=null),this._bondStart!==null&&(this._editor.fire(\"bond:cancel\",{start:this._bondStart}),this._editor.fire(\"bond:preview-end\",{start:this._bondStart}),this._bondStart=null,this._bondDragMoved=false),this._dragOrigin=null,this._panStart=null,this._atomDragState=null,this._panMoved=false,this._atomDragMoved=false,st(this._nextAddCursorEl);}_openChooseR(e,t,n,o,r){this._chooseRDialog===null&&(this._chooseRDialog=new Ke(this._editor)),this._chooseRDialog.open(e,t,{freeR1:o,freeR2:r}).then(a=>{if(!this._destroyed){if(a===null){this._editor.fire(\"bond:cancel\",{start:e});return}try{this._editor.addBond(e,t,a.r1,a.r2,n);}catch{this._editor.fire(\"bond:cancel\",{start:e});}}});}_updateNextAddCursor(e){let t=this._editor.getNextAddSymbol(),n=this._editor.getMode(),o=this._hoverAtom!==null,r=this._bondStart!==null||this._dragOrigin!==null||this._panStart!==null||this._atomDragState!==null;if(!(n===\"select\"&&t!==null&&!o&&!r)){this._nextAddCursorEl!==null&&st(this._nextAddCursorEl);return}let a=this._host.ownerDocument;if(a===null)return;this._nextAddCursorEl===null&&(this._nextAddCursorEl=Ti(a));let d=this._editor.getService().monomerLib,l=null;for(let u of d.getPolymerTypes()){let c=d.getMonomer(u,t.symbol);if(c!==null){l=c;break}}Si(this._nextAddCursorEl,t.symbol,t.biotype,l,this._editor._currentTheme(),e.clientX,e.clientY);}_addsEnabled(){return this._editor.getMode()===\"select\"}_handleWheel(e){let t=e.ctrlKey===true||e.metaKey===true;if(e.preventDefault(),t){this._wheelPan(e);return}let n=e.deltaY<0?1.1:1/1.1,o=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),r=this._editor.getViewport(),s=r.scale===0?o:{x:(o.x-r.offset.x)/r.scale,y:(o.y-r.offset.y)/r.scale};this._editor.zoom(n,s);}_wheelPan(e){let t=e.deltaX??0,n=e.deltaY??0;if(t===0&&n===0)return;let o=this._toViewBox({clientX:e.clientX,clientY:e.clientY}),r=this._toViewBox({clientX:e.clientX+t,clientY:e.clientY+n}),s=r.x-o.x,a=r.y-o.y,d=this._editor.getViewport();this._editor.panTo({x:d.offset.x-s,y:d.offset.y-a});}_toModel(e){let t=this._host.querySelector(\"svg\"),n=t!==null?t.querySelector(\".hw-content\"):null;if(t!==null&&n!==null){let r=Ci(n,e.clientX,e.clientY);if(r!==null)return r;let s=this._host.getBoundingClientRect(),a=e.clientX-s.left,d=e.clientY-s.top,l=Ca(n.getAttribute(\"transform\")??\"\");return l!==null?{x:(a-l.tx)/(l.scale===0?1:l.scale),y:(d-l.ty)/(l.scale===0?1:l.scale)}:{x:a,y:d}}let o=this._host.getBoundingClientRect();return {x:e.clientX-o.left,y:e.clientY-o.top}}_toViewBox(e){let t=this._host.querySelector(\"svg\");if(t!==null){let o=Ci(t,e.clientX,e.clientY);if(o!==null)return o;let r=this._host.getBoundingClientRect(),s=e.clientX-r.left,a=e.clientY-r.top,d=Ea(t.getAttribute(\"viewBox\"));return d!==null&&r.width>0&&r.height>0?{x:s*(d.w/r.width),y:a*(d.h/r.height)}:{x:s,y:a}}let n=this._host.getBoundingClientRect();return {x:e.clientX-n.left,y:e.clientY-n.top}}};function Ei(i,e,t,n){let o=be(i),r=be(e);if(o===0||r===0)return {mode:\"auto\",r1:2,r2:1,kind:n};let s=W(i,t),a=W(e,t);if(s.length===0)return {mode:\"fail\",reason:`${i.symbol} has no free R-groups (max ${o}).`};if(a.length===0)return {mode:\"fail\",reason:`${e.symbol} has no free R-groups (max ${r}).`};if(s.includes(2)&&a.includes(1)&&(s.length===1||a.length===1))return {mode:\"auto\",r1:2,r2:1,kind:n};if(s.length===1&&a.length===1){let d=s[0],l=a[0];return {mode:\"auto\",r1:d,r2:l,kind:n}}return {mode:\"choose\",freeR1:s,freeR2:a}}function Ci(i,e,t){let n=i;if(typeof n.getScreenCTM!=\"function\")return null;let o=n.getScreenCTM();if(o===null)return null;let r=null;try{let d=o;typeof d.inverse==\"function\"&&(r=d.inverse());}catch{return null}if(r===null)return null;let s=n.ownerSVGElement;if(s!=null&&typeof s.createSVGPoint==\"function\"){let d=s.createSVGPoint();d.x=e,d.y=t;let l=d.matrixTransform(r);return {x:l.x,y:l.y}}let a=r;return {x:a.a*e+a.c*t+a.e,y:a.b*e+a.d*t+a.f}}function Ea(i){if(i===null||i===\"\")return null;let e=i.split(/[,\\s]+/).map(o=>Number(o)).filter(o=>Number.isFinite(o));if(e.length<4)return null;let t=e[2],n=e[3];return t<=0||n<=0?null:{w:t,h:n}}function Ca(i){if(i===\"\")return null;let e=0,t=0,n=1,o=/(translate|scale)\\(([^)]+)\\)/g,r,s=false;for(;(r=o.exec(i))!==null;){s=true;let a=r[1],d=(r[2]??\"\").split(/[,\\s]+/).map(l=>Number(l)).filter(l=>Number.isFinite(l));if(a===\"translate\"){let l=d[0]??0,u=d[1]??0;e=e+n*l,t=t+n*u;}else if(a===\"scale\"){let l=d[0]??1;n=n*l;}}return s?{tx:e,ty:t,scale:n}:null}function Li(i,e,t){if(i.bio.chainId!==e.bio.chainId)return  false;let n=t.chains.find(s=>s.id===i.bio.chainId);if(n===void 0)return  false;let o=-1,r=-1;for(let s=0;s<n.backboneAtoms.length;s++){let a=n.backboneAtoms[s];a.id===i.id&&(o=s),a.id===e.id&&(r=s);}return o<0||r<0?false:Math.abs(o-r)===1}function Bi(i){return {shift:i.shiftKey===true,alt:i.altKey===true,ctrl:i.ctrlKey===true,meta:i.metaKey===true}}function Ri(i,e){let t=Math.min(i.x,e.x),n=Math.min(i.y,e.y);return {x:t,y:n,width:Math.abs(i.x-e.x),height:Math.abs(i.y-e.y)}}var Wt=class{constructor(e,t,n){this._destroyed=false;this._host=e,this._editor=t,this._enabled=n?.enableKeyboard!==false,this._enabled&&e.getAttribute(\"tabindex\")===null&&e.setAttribute(\"tabindex\",\"0\"),this._onKey=o=>this._handleKey(o),e.addEventListener(\"keydown\",this._onKey);}destroy(){this._destroyed||(this._destroyed=true,this._host.removeEventListener(\"keydown\",this._onKey));}_handleKey(e){if(!this._enabled)return;let t=this._classify(e),n=La(e);if(t===null){this._editor.fire(\"key:unhandled\",{key:e.key,modifiers:n,preventDefault:()=>e.preventDefault()});return}let o=false,r=()=>{o=true,e.preventDefault();};this._editor.fire(\"key:command\",{command:t,preventDefault:r}),!o&&(e.preventDefault(),t!==\"clearSelection\"&&(e.stopPropagation(),e.stopImmediatePropagation?.()),this._execute(t));}_classify(e){let t=e.key,n=e.ctrlKey||e.metaKey;return t===\"Delete\"||t===\"Backspace\"?\"delete\":n&&(t===\"z\"||t===\"Z\")&&!e.shiftKey?\"undo\":n&&((t===\"z\"||t===\"Z\")&&e.shiftKey||t===\"y\"||t===\"Y\")?\"redo\":n&&(t===\"a\"||t===\"A\")?\"selectAll\":n&&(t===\"c\"||t===\"C\")?\"copy\":n&&(t===\"v\"||t===\"V\")?\"paste\":n&&(t===\"x\"||t===\"X\")?\"cut\":t===\"Escape\"?\"clearSelection\":t===\"+\"||t===\"=\"?\"zoomIn\":t===\"-\"||t===\"_\"?\"zoomOut\":t===\"0\"?\"fitToContent\":t===\"ArrowUp\"?\"nudgeUp\":t===\"ArrowDown\"?\"nudgeDown\":t===\"ArrowLeft\"?\"nudgeLeft\":t===\"ArrowRight\"?\"nudgeRight\":null}_execute(e){switch(e){case \"delete\":this._editor.deleteSelection();return;case \"undo\":this._editor.undo();return;case \"redo\":this._editor.redo();return;case \"selectAll\":this._editor.selectAll();return;case \"clearSelection\":this._editor.clearSelection();return;case \"zoomIn\":this._editor.zoom(1.1);return;case \"zoomOut\":this._editor.zoom(1/1.1);return;case \"fitToContent\":this._editor.fitToContent();return;case \"nudgeUp\":this._editor.nudgeSelection(0,-5);return;case \"nudgeDown\":this._editor.nudgeSelection(0,5);return;case \"nudgeLeft\":this._editor.nudgeSelection(-5,0);return;case \"nudgeRight\":this._editor.nudgeSelection(5,0);return;case \"copy\":{let t=this._editor.getHelm();this._editor.fire(\"clipboard:copy\",{format:\"helm\",payload:t});return}case \"cut\":{let t=this._editor.getHelm();this._editor.fire(\"clipboard:copy\",{format:\"helm\",payload:t}),this._editor.deleteSelection();return}case \"paste\":this._editor.fire(\"clipboard:paste\",{format:\"helm\"});return;default:return}}};function La(i){return {shift:i.shiftKey===true,alt:i.altKey===true,ctrl:i.ctrlKey===true,meta:i.metaKey===true}}var Ba=\"application/x-hwe-monomer\",jt=class{constructor(e,t){this._currentPaletteSymbol=null;this._currentPaletteBiotype=null;this._destroyed=false;this._unsubs=[];this._host=e,this._editor=t,this._tester=new q(t.getMol(),t._currentTheme()),this._unsubs.push(t.on(\"mol:changed\",()=>{this._tester=new q(this._editor.getMol(),this._editor._currentTheme());})),this._onDragOver=n=>this._handleDragOver(n),this._onDrop=n=>this._handleDrop(n),this._onDragStart=n=>this._handleDragStart(n),this._onDragEnd=n=>this._handleDragEnd(n),this._onDragEnter=n=>this._handleDragEnter(n),this._onDragLeave=n=>this._handleDragLeave(n),e.addEventListener(\"dragover\",this._onDragOver),e.addEventListener(\"drop\",this._onDrop),e.addEventListener(\"dragstart\",this._onDragStart),e.addEventListener(\"dragend\",this._onDragEnd),e.addEventListener(\"dragenter\",this._onDragEnter),e.addEventListener(\"dragleave\",this._onDragLeave);}startPaletteDrag(e,t){this._currentPaletteSymbol=e,this._currentPaletteBiotype=t,this._editor.fire(\"dnd:start\",{source:\"palette\",symbol:e});}cancelPaletteDrag(){this._currentPaletteSymbol!==null&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire(\"dnd:cancel\",{source:\"palette\"}));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this._host.removeEventListener(\"dragover\",this._onDragOver),this._host.removeEventListener(\"drop\",this._onDrop),this._host.removeEventListener(\"dragstart\",this._onDragStart),this._host.removeEventListener(\"dragend\",this._onDragEnd),this._host.removeEventListener(\"dragenter\",this._onDragEnter),this._host.removeEventListener(\"dragleave\",this._onDragLeave);}}_activePaletteSymbol(e){if(this._currentPaletteSymbol!==null&&this._currentPaletteBiotype!==null)return {symbol:this._currentPaletteSymbol,biotype:this._currentPaletteBiotype};let t=e.dataTransfer;if(t==null)return null;try{let n=typeof t.getData==\"function\"?t.getData(Ba):\"\";if(n===\"\")return null;let o=JSON.parse(n);return typeof o.symbol!=\"string\"||typeof o.biotype!=\"string\"?null:{symbol:o.symbol,biotype:o.biotype}}catch{return null}}_handleDragEnter(e){if(this._activePaletteSymbol(e)!==null&&(e.preventDefault(),e.dataTransfer!==null&&e.dataTransfer!==void 0))try{e.dataTransfer.dropEffect=\"copy\";}catch{}}_handleDragLeave(e){}_handleDragOver(e){if(this._activePaletteSymbol(e)===null)return;if(e.preventDefault(),e.dataTransfer!==null&&e.dataTransfer!==void 0)try{e.dataTransfer.dropEffect=\"copy\";}catch{}let n=this._toModel(e),o=this._tester.test(n),r=o?.atom!==void 0?o.atom:o?.bond!==void 0?o.bond:void 0,s={clientX:e.clientX,clientY:e.clientY};r!==void 0&&(s.target=r),this._editor.fire(\"dnd:over\",s);}_handleDrop(e){let t=this._activePaletteSymbol(e);if(t===null)return;e.preventDefault();let{symbol:n,biotype:o}=t,r=this._toModel(e),s=this._tester.test(r),a=s?.atom!==void 0?s.atom:s?.bond!==void 0?s.bond:void 0,d={symbol:n,biotype:o,clientX:e.clientX,clientY:e.clientY};a!==void 0&&(d.target=a),this._editor.fire(\"dnd:drop\",d),s?.atom!==void 0?this._editor.replaceMonomer(s.atom,n):this._editor.addAtom(r,o,n),this._currentPaletteSymbol=null,this._currentPaletteBiotype=null;}_handleDragStart(e){this._editor.fire(\"dnd:start\",{source:\"canvas\"});}_handleDragEnd(e){this._currentPaletteSymbol!==null&&(this._currentPaletteSymbol=null,this._currentPaletteBiotype=null,this._editor.fire(\"dnd:cancel\",{source:\"palette\"}));}_toModel(e){let t=this._host.querySelector(\"svg\"),n=t!==null?t.querySelector(\".hw-content\"):null;if(t!==null&&n!==null){let r=Ra(n,e.clientX,e.clientY);if(r!==null)return r;let s=this._host.getBoundingClientRect(),a=e.clientX-s.left,d=e.clientY-s.top,l=Ia(n.getAttribute(\"transform\")??\"\");return l!==null?{x:(a-l.tx)/(l.scale===0?1:l.scale),y:(d-l.ty)/(l.scale===0?1:l.scale)}:{x:a,y:d}}let o=this._host.getBoundingClientRect();return {x:e.clientX-o.left,y:e.clientY-o.top}}};function Ra(i,e,t){let n=i;if(typeof n.getScreenCTM!=\"function\")return null;let o=n.getScreenCTM();if(o===null)return null;let r=null;try{let d=o;typeof d.inverse==\"function\"&&(r=d.inverse());}catch{return null}if(r===null)return null;let s=n.ownerSVGElement;if(s!=null&&typeof s.createSVGPoint==\"function\"){let d=s.createSVGPoint();d.x=e,d.y=t;let l=d.matrixTransform(r);return {x:l.x,y:l.y}}let a=r;return {x:a.a*e+a.c*t+a.e,y:a.b*e+a.d*t+a.f}}function Ia(i){if(i===\"\")return null;let e=0,t=0,n=1,o=/(translate|scale)\\(([^)]+)\\)/g,r,s=false;for(;(r=o.exec(i))!==null;){s=true;let a=r[1],d=(r[2]??\"\").split(/[,\\s]+/).map(l=>Number(l)).filter(l=>Number.isFinite(l));if(a===\"translate\"){let l=d[0]??0,u=d[1]??0;e=e+n*l,t=t+n*u;}else if(a===\"scale\"){let l=d[0]??1;n=n*l;}}return s?{tx:e,ty:t,scale:n}:null}var We=class{constructor(e,t){this._modal=null;this._atom=null;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"AtomPropsDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}get isOpen(){return this._modal!==null&&this._modal.isOpen}open(e){this.close(),this._atom=e;let t=this._editor._getHost();if(t===null)return;let n=new X(t,{documentImpl:this._doc,title:\"Monomer Properties\",testId:\"atom-props\"});this._modal=n;let o=v(this._doc,\"div\",{class:\"hw-modal__info\"},[`Position ${e.bio.continuousId} in ${e.bio.chainId}`]),r=Ve(this._doc,\"Symbol\",e.symbol,\"atom-props-symbol\"),s=Ve(this._doc,\"Annotation\",e.bio.annotation??\"\",\"atom-props-annotation\"),a=ze(this._doc,\"atom-props\"),d=()=>this._commit(r.input.value,s.input.value);a.ok.addEventListener(\"click\",d),a.cancel.addEventListener(\"click\",()=>this.close()),n.setPrimaryAction(d),n.body.appendChild(o),n.body.appendChild(r.row),n.body.appendChild(s.row),n.body.appendChild(a.row),n.open();}close(){this._modal!==null&&(this._modal.close(),this._modal=null),this._atom=null;}_commit(e,t){let n=this._atom;if(n===null){this.close();return}let o=e.trim(),r=(n.bio.annotation??\"\")!==t;if(o.length>0&&o!==n.symbol&&this._editor.replaceMonomer(n,o),r){let a=new N(this._editor.getMol()),d={};d.tag=t===\"\"?void 0:t,a.updateAtom(n.id,d);let{mol:l}=a.commit();this._editor.setMol(l);let u=l.atoms.find(c=>c.id===n.id);if(u!==void 0){let c={atom:u};n.bio.annotation!==void 0&&(c.oldAnnotation=n.bio.annotation),t!==\"\"&&(c.newAnnotation=t),this._editor.fire(\"monomer:annotate\",c);}}this.close();}};var je=class{constructor(e,t){this._modal=null;this._bond=null;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"BondPropsDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}get isOpen(){return this._modal!==null&&this._modal.isOpen}open(e){this.close(),this._bond=e;let t=this._editor._getHost();if(t===null)return;let n=new X(t,{documentImpl:this._doc,title:\"Bond Properties\",testId:\"bond-props\"});this._modal=n;let o=v(this._doc,\"div\",{class:\"hw-modal__info\"},[`Kind: ${e.kind}`]),r=this._buildAtomsPreviewRow(e),s=e.r1.kind===\"numeric\",a=e.r2.kind===\"numeric\",d=s&&a,u=this._editor.getMol().bonds,c=d?Ii(e.r1,e.a1,u):[],m=d?Ii(e.r2,e.a2,u):[],p=null,h=null;if(d){let _=String(e.r1.r),b=String(e.r2.r);p=Ue(this._doc,`R-group on ${e.a1.symbol} (${e.a1.bio.chainId}:${e.a1.bio.positionInChain})`,c,_,\"bond-props-r1\"),h=Ue(this._doc,`R-group on ${e.a2.symbol} (${e.a2.bio.chainId}:${e.a2.bio.positionInChain})`,m,b,\"bond-props-r2\");}let y=ze(this._doc,\"bond-props\"),f=()=>{let _=p!==null?Number(Pi(p.select,e.r1.r)):null,b=h!==null?Number(Pi(h.select,e.r2.r)):null;this._commit(_,b);};y.ok.addEventListener(\"click\",f),y.cancel.addEventListener(\"click\",()=>this.close()),n.setPrimaryAction(f),n.body.appendChild(o),r!==null&&n.body.appendChild(r),p!==null&&n.body.appendChild(p.row),h!==null&&n.body.appendChild(h.row),n.body.appendChild(y.row),n.open();}_buildAtomsPreviewRow(e){let t=this._rdkit(),n=this._buildAtomCell(e.a1,t,\"bond-props-atom-a1\"),o=this._buildAtomCell(e.a2,t,\"bond-props-atom-a2\"),r=v(this._doc,\"div\",{class:\"hw-bond-props__bond-arrow\"},[\"\\u2194\"]);return v(this._doc,\"div\",{class:\"hw-bond-props__atoms\",\"data-testid\":\"bond-props-atoms\"},[n,r,o])}_buildAtomCell(e,t,n){let o=e.monomer?.name??e.symbol,r=e.symbol===o?e.symbol:`${e.symbol} \\u2014 ${o}`,s=v(this._doc,\"div\",{class:\"hw-bond-props__atom-label\"},[r]),a={class:\"hw-bond-props__atom-rdkit\",\"data-testid\":`${n}-rdkit`},d=v(this._doc,\"div\",a),l=e.monomer?.smiles;if(t!==null&&l!==void 0&&l!==\"\"){let u=ye(t,l,220,140);u!==null&&u!==\"\"&&(d.innerHTML=u);}return v(this._doc,\"div\",{class:\"hw-bond-props__atom\",\"data-testid\":n},[s,d])}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}close(){this._modal!==null&&(this._modal.close(),this._modal=null),this._bond=null;}_commit(e,t){let n=this._bond;if(n===null){this.close();return}let o=n.r1.kind===\"numeric\"?n.r1.r:null,r=n.r2.kind===\"numeric\"?n.r2.r:null;if(!(e!==null&&t!==null&&(e!==o||t!==r))){this.close();return}if(e!==null&&t!==null){let a=n.kind,d=n.a1,l=n.a2;this._editor.removeBond(n);try{this._editor.addBond(d,l,e,t,a);}catch(u){if(o!==null&&r!==null)try{this._editor.addBond(d,l,o,r,n.kind);}catch{}}}this.close();}};function Ii(i,e,t){let n=e.monomer?.rgroups;if(n===void 0||n.length===0)return [{value:\"1\",label:\"R1\"},{value:\"2\",label:\"R2\"},{value:\"3\",label:\"R3\"}];let o=new Set(W(e,t));o.add(i.r);let r=Array.from(o).sort((a,d)=>a-d),s=[];for(let a of r){let d=n[a-1];if(d===void 0)continue;let l=d.capGroupName!==void 0&&d.capGroupName!==\"\"?` (${d.capGroupName})`:\"\";s.push({value:String(a),label:`${d.label}${l}`});}return s}function Pi(i,e){let t=i.value;if(typeof t==\"string\"&&t.length>0){let o=Number(t);if(Number.isFinite(o)&&o>=1)return o}let n=i.querySelectorAll(\"option\");for(let o of Array.from(n))if(o.getAttribute(\"selected\")!==null){let r=o.getAttribute(\"value\")??\"\",s=Number(r);if(Number.isFinite(s)&&s>=1)return s}return e}var qe=class{constructor(e,t){this._modal=null;this._result=null;this._findInput=null;this._replaceInput=null;this._matches=[];this._cursor=-1;this._editor=e;let n=e._getHost();if(n===null)throw new Error(\"FindReplaceDialog: editor has no host element.\");this._doc=t?.documentImpl??S(n);}get isOpen(){return this._modal!==null&&this._modal.isOpen}open(){this.close();let e=this._editor._getHost();if(e===null)return;let t=new X(e,{documentImpl:this._doc,title:\"Find / Replace\",testId:\"find-replace\"});this._modal=t;let n=Ve(this._doc,\"Find\",\"\",\"find-replace-find\"),o=Ve(this._doc,\"Replace with\",\"\",\"find-replace-replace\");this._findInput=n.input,this._replaceInput=o.input;let r=this._doc.createElement(\"button\");r.setAttribute(\"class\",\"hw-modal__find-next\"),r.setAttribute(\"type\",\"button\"),r.setAttribute(\"data-testid\",\"find-replace-next\"),r.appendChild(this._doc.createTextNode(\"Find Next\")),r.addEventListener(\"click\",()=>this._findNext());let s=this._doc.createElement(\"button\");s.setAttribute(\"class\",\"hw-modal__replace\"),s.setAttribute(\"type\",\"button\"),s.setAttribute(\"data-testid\",\"find-replace-replace-one\"),s.appendChild(this._doc.createTextNode(\"Replace\")),s.addEventListener(\"click\",()=>this._replaceOne());let a=this._doc.createElement(\"button\");a.setAttribute(\"class\",\"hw-modal__replace-all\"),a.setAttribute(\"type\",\"button\"),a.setAttribute(\"data-testid\",\"find-replace-replace-all\"),a.appendChild(this._doc.createTextNode(\"Replace All\")),a.addEventListener(\"click\",()=>this._replaceAll());let d=this._doc.createElement(\"button\");d.setAttribute(\"class\",\"hw-modal__cancel\"),d.setAttribute(\"type\",\"button\"),d.setAttribute(\"data-testid\",\"find-replace-close\"),d.appendChild(this._doc.createTextNode(\"Close\")),d.addEventListener(\"click\",()=>this.close());let l=v(this._doc,\"div\",{class:\"hw-modal__actions\"},[r,s,a,d]),u=v(this._doc,\"div\",{class:\"hw-modal__result\",\"data-testid\":\"find-replace-result\"},[\"0 matches\"]);this._result=u,t.setPrimaryAction(()=>this._findNext()),t.body.appendChild(n.row),t.body.appendChild(o.row),t.body.appendChild(l),t.body.appendChild(u),t.open();}close(){this._modal!==null&&(this._modal.close(),this._modal=null),this._result=null,this._findInput=null,this._replaceInput=null,this._matches=[],this._cursor=-1;}_findNext(){let e=this._findInput?.value.trim()??\"\";if(e===\"\"){this._setResultText(\"Enter a symbol to find\");return}let t=this._editor.findMonomers(e);if(this._matches=t.map(o=>o.id),this._matches.length===0){this._cursor=-1,this._editor.setHighlights([]),this._setResultText(\"No matches\");return}this._cursor=(this._cursor+1)%this._matches.length;let n=this._matches[this._cursor];n!==void 0&&this._editor.setHighlights([n]),this._setResultText(`${this._cursor+1} / ${this._matches.length} matches`);}_replaceOne(){let e=this._findInput?.value.trim()??\"\",t=this._replaceInput?.value.trim()??\"\";if(e===\"\"||t===\"\"){this._setResultText(\"Both Find and Replace fields are required\");return}if(this._matches.length===0||this._cursor<0){this._findNext();return}let n=this._matches[this._cursor];if(n===void 0)return;let o=this._editor.getMol().atoms.find(r=>r.id===n);if(o!==void 0)if(this._editor.replaceMonomer(o,t),this._matches.splice(this._cursor,1),this._matches.length===0)this._cursor=-1,this._editor.setHighlights([]),this._setResultText(\"Replaced; no further matches\");else {this._cursor=this._cursor%this._matches.length;let r=this._matches[this._cursor];r!==void 0&&this._editor.setHighlights([r]),this._setResultText(`${this._matches.length} matches remaining`);}}_replaceAll(){let e=this._findInput?.value.trim()??\"\",t=this._replaceInput?.value.trim()??\"\";if(e===\"\"||t===\"\"){this._setResultText(\"Both Find and Replace fields are required\");return}let n=this._editor.replaceMonomers(e,t);this._matches=[],this._cursor=-1,this._editor.setHighlights([]),this._setResultText(`${n} replacement${n===1?\"\":\"s\"} made`);}_setResultText(e){if(this._result!==null){for(;this._result.firstChild!==null;)this._result.removeChild(this._result.firstChild);this._result.appendChild(this._doc.createTextNode(e));}}};var ge=Object.freeze(new Set),Pa=.2,Ha=8,at=class{constructor(e,t){this._events=new Fe;this._destroyed=false;this._view=null;this._pointer=null;this._keyboard=null;this._dnd=null;this._atomDialog=null;this._bondDialog=null;this._findReplaceDialog=null;this._viewBootstrapped=false;this._mode=\"select\";this._nextAdd=null;this._lastAction=null;this._lastTripletSugarPos=null;if(t.service===void 0||t.service===null)throw new TypeError(\"HelmEditor: options.service is required\");this._host=e,this._service=t.service,this._options=Object.freeze({...t}),this._mol=me(),this._selection=V.empty(),this._highlights=ge,this._theme=t.service.theme??$,this._viewport={scale:1,offset:{x:0,y:0}},this._viewOnly=t.viewOnly??false,this._history=new Ge({maxEntries:100}),this._history.push({mol:this._mol,label:\"initial\"}),this._libUnsub=this._service.monomerLib.onChanged.subscribe(n=>{let o=this._service.monomerLib,r=typeof o.version==\"number\"?o.version:0,s=n.type===\"reload\"?\"replace\":\"update\";this._events.fire(\"monomer-lib:change\",{source:this._service.monomerLib.source,version:r,reason:s});}),t.initialHelm!==void 0&&this.setHelm(t.initialHelm),this._bootstrapWaveB();}_bootstrapWaveB(){if(this._viewBootstrapped||this._host===null)return;let e=this._resolveDocument(this._host);if(e===null)return;this._viewBootstrapped=true;let t={documentImpl:e};this._options.width!==void 0&&(t.width=this._options.width),this._options.height!==void 0&&(t.height=this._options.height),this._view=new Vt(this._host,this,t),this._viewOnly!==true&&(this._pointer=new Kt(this._host,this,{enableContextMenu:this._options.enableContextMenu??true})),this._options.enableKeyboard!==false&&(this._keyboard=new Wt(this._host,this,{enableKeyboard:true})),this._options.enableDragDrop!==false&&(this._dnd=new jt(this._host,this)),this._events.on(\"monomer:hover\",n=>{this.setHighlights([n.atom.id]);}),this._events.on(\"monomer:hover-end\",()=>{this.clearHighlights();}),this._events.on(\"monomer:click\",n=>{let o=n.modifiers;if(o.ctrl===true||o.meta===true){this.setSelection(V.toggle(this._selection,{kind:\"atom\",id:n.atom.id}));return}if(o.shift===true){this.setSelection(V.union(this._selection,V.fromAtoms([n.atom.id])));return}this.setSelection(V.fromAtoms([n.atom.id]));});}_resolveDocument(e){let t=e.ownerDocument;if(t!=null)return t;let n=globalThis;return n.document!==void 0?n.document:null}destroy(){this._destroyed||(this._destroyed=true,this._atomDialog!==null&&(this._atomDialog.close(),this._atomDialog=null),this._bondDialog!==null&&(this._bondDialog.close(),this._bondDialog=null),this._findReplaceDialog!==null&&(this._findReplaceDialog.close(),this._findReplaceDialog=null),this._dnd!==null&&(this._dnd.destroy(),this._dnd=null),this._keyboard!==null&&(this._keyboard.destroy(),this._keyboard=null),this._pointer!==null&&(this._pointer.destroy(),this._pointer=null),this._view!==null&&(this._view.destroy(),this._view=null),this._libUnsub(),this._events.clear(),this._history.clear());}resize(e,t){this._ensureLive(),this._view!==null&&this._view.resize(e,t),this._events.fire(\"view:resize\",{width:e,height:t});}redraw(){if(this._ensureLive(),this._view!==null){this._view.redraw();return}this._events.fire(\"render:skip\",{reason:\"no-view-mounted\"});}setHelm(e,t){this._ensureLive();let n=t?.canonicalize??this._options.canonicalize??false,o=this._service.parse(e,{mode:\"lenient\"}),r=o.diagnostics;r.filter(l=>l.severity===\"error\").length>0&&this._events.fire(\"helm:parse-error\",{helm:e,diagnostics:r});for(let l of r)l.severity===\"error\"?this._events.fire(\"validation:error\",{diagnostic:l}):l.severity===\"warning\"&&this._events.fire(\"validation:warning\",{diagnostic:l});let a=o.mol;if(n){let l=this._service.canonicalize(e);a=this._service.parse(l,{mode:\"lenient\"}).mol;}let d=oe(a,this._options.bondLength!==void 0?{bondLength:this._options.bondLength}:void 0);return this._replaceMol(d,\"setHelm\",\"api\"),{mol:d,diagnostics:r}}getHelm(e){this._ensureLive();let t={};return e?.canonicalize!==void 0&&(t.canonicalize=e.canonicalize),e?.includeHighlights!==void 0&&(t.includeHighlights=e.includeHighlights),this._service.serialize(this._mol,t)}setMol(e){this._ensureLive(),this._replaceMol(e,\"setMol\",\"api\");}getMol(){return this._mol}getService(){return this._service}getSelection(){return this._selection}setSelection(e){if(this._ensureLive(),V.equals(this._selection,e))return;let t=V.difference(e,this._selection),n=V.difference(this._selection,e);this._selection=e,this._events.fire(\"selection:change\",{selection:e,addedAtomIds:t.atoms,removedAtomIds:n.atoms,addedBondIds:t.bonds,removedBondIds:n.bonds});}selectAll(){this._ensureLive();let e=this._mol.atoms.map(n=>n.id),t=this._mol.bonds.map(n=>n.id);this.setSelection(V.fromAtomsAndBonds(e,t));}clearSelection(){this._ensureLive(),!this._selection.isEmpty&&this.setSelection(V.empty());}setHighlights(e){this._ensureLive();let t=new Set(e);this._highlights=t,this._events.fire(\"highlight:change\",{atomIds:t,bondIds:ge});}clearHighlights(){this._ensureLive(),this._highlights.size!==0&&(this._highlights=ge,this._events.fire(\"highlight:change\",{atomIds:ge,bondIds:ge}));}addAtom(e,t,n){this._ensureLive();let o=new N(this._mol),r=o.addAtom({p:e,biotype:t,symbol:n}),{mol:s}=o.commit(),a=ke(s,this._service.monomerLib,{mode:\"lenient\"}).mol;this._replaceMol(a,`addAtom:${n}`,\"api\");let d=J(a,r);if(d===void 0)throw new Error(\"HelmEditor.addAtom: lost atom after commit\");return this._events.fire(\"monomer:add\",{atom:d,source:\"api\"}),d}removeAtom(e){this._ensureLive();let t=typeof e==\"number\"?e:e.id,n=J(this._mol,t);if(n===void 0)return;let o=new N(this._mol);o.removeAtom(t);let{mol:r}=o.commit();this._replaceMol(r,`removeAtom:${n.symbol}`,\"api\"),this._events.fire(\"monomer:remove\",{atom:n,source:\"api\"});}addBond(e,t,n,o,r){this._ensureLive();let s,a;try{this._validateAddBondConstraints(e,t,n,o);let l=r??\"backbone\",u=this._maybeMergeForLinearExtend(e,t,n,o,l);if(u!==null)({id:s,mol:a}=u);else {let c=new N(this._mol);s=c.addBond({a1:e.id,a2:t.id,kind:r??\"backbone\",r1:{kind:\"numeric\",r:n},r2:{kind:\"numeric\",r:o}}),{mol:a}=c.commit();}}catch(l){let u=l instanceof P?l.message:this._friendlyBondError(l instanceof Error?l.message:String(l),e,t,n,o);throw this._events.fire(\"editor:status\",{message:`Could not add bond: ${u}`,severity:\"error\",durationMs:3e3}),l}this._replaceMol(a,\"addBond\",\"api\");let d=xt(a,s);if(d===void 0)throw new Error(\"HelmEditor.addBond: lost bond after commit\");return this._events.fire(\"bond:add\",{bond:d,source:\"api\"}),d}_maybeMergeForLinearExtend(e,t,n,o,r){if(e.bio.chainId===t.bio.chainId||r!==\"backbone\"&&r!==\"cross-polymer\")return null;let s=this._mol.chains.find(d=>d.id===e.bio.chainId),a=this._mol.chains.find(d=>d.id===t.bio.chainId);if(s===void 0||a===void 0||s.polymerType!==a.polymerType||s.polymerType===x.CHEM||s.polymerType===x.BLOB)return null;if(n===2&&o===1){let d=s.backboneAtoms[s.backboneAtoms.length-1],l=a.backboneAtoms[0];if(d!==void 0&&l!==void 0&&d.id===e.id&&l.id===t.id)return this._mergeChains(s,a,r)}if(n===1&&o===2){let d=s.backboneAtoms[0],l=a.backboneAtoms[a.backboneAtoms.length-1];if(d!==void 0&&l!==void 0&&d.id===e.id&&l.id===t.id)return this._mergeChains(a,s,r)}return null}_mergeChains(e,t,n){let o=e.backboneAtoms.length,r=new Set;for(let b of t.backboneAtoms)r.add(b.id),b.branchAtom!==void 0&&r.add(b.branchAtom.id);let s=new Map,a=o;for(let b of t.backboneAtoms){a+=1;let A={...b,bio:{...b.bio,chainId:e.id,positionInChain:a}};if(s.set(b.id,A),b.branchAtom!==void 0){let w=b.branchAtom,k={...w,bio:{...w.bio,chainId:e.id,positionInChain:a}};s.set(w.id,k);}}for(let b of t.backboneAtoms){let A=s.get(b.id);if(A===void 0||b.branchAtom===void 0)continue;let w=s.get(b.branchAtom.id);w!==void 0&&(A.branchAtom=w);}for(let b of this._mol.atoms)s.has(b.id)||s.set(b.id,b);let d=0;for(let b of this._mol.atoms)b.id>d&&(d=b.id);for(let b of this._mol.bonds)b.id>d&&(d=b.id);let l=d+1,u=s.get(e.backboneAtoms[e.backboneAtoms.length-1].id),c=s.get(t.backboneAtoms[0].id),m={id:l,a1:u,a2:c,kind:\"backbone\",r1:{kind:\"numeric\",r:2},r2:{kind:\"numeric\",r:1}},p=[];for(let b of this._mol.bonds){let A=s.get(b.a1.id)??b.a1,w=s.get(b.a2.id)??b.a2;A===b.a1&&w===b.a2?p.push(b):p.push({...b,a1:A,a2:w});}p.push(m);let h=[],y=[...e.backboneAtoms];for(let b of t.backboneAtoms)y.push(s.get(b.id));for(let b of this._mol.chains)if(b.id!==t.id)if(b.id===e.id){let A=b.bonds.map(w=>{let k=s.get(w.a1.id)??w.a1,C=s.get(w.a2.id)??w.a2;return k===w.a1&&C===w.a2?w:{...w,a1:k,a2:C}});for(let w of t.bonds){let k=s.get(w.a1.id)??w.a1,C=s.get(w.a2.id)??w.a2;A.push(k===w.a1&&C===w.a2?w:{...w,a1:k,a2:C});}A.push(m),h.push({id:b.id,polymerType:b.polymerType,backboneAtoms:y,bonds:A,...b.annotation!==void 0?{annotation:b.annotation}:{}});}else {let A=b.backboneAtoms.map(k=>s.get(k.id)??k),w=b.bonds.map(k=>{let C=s.get(k.a1.id)??k.a1,I=s.get(k.a2.id)??k.a2;return C===k.a1&&I===k.a2?k:{...k,a1:C,a2:I}});h.push({id:b.id,polymerType:b.polymerType,backboneAtoms:A,bonds:w,...b.annotation!==void 0?{annotation:b.annotation}:{}});}let _={atoms:this._mol.atoms.map(b=>s.get(b.id)??b),bonds:p,chains:h,groups:this._mol.groups,annotations:this._mol.annotations};return _=this._refreshContinuousIdsLocal(_),{id:l,mol:_}}_refreshContinuousIdsLocal(e){let t=Le(e),n=new Map;for(let d of e.atoms){let l=t.get(d.id);if(l===void 0||l===d.bio.continuousId){n.set(d.id,d);continue}n.set(d.id,{...d,bio:{...d.bio,continuousId:l}});}for(let d of e.atoms){if(d.branchAtom===void 0)continue;let l=n.get(d.id),u=n.get(d.branchAtom.id);l===void 0||u===void 0||(l.branchAtom=u);}let o=e.bonds.map(d=>{let l=n.get(d.a1.id)??d.a1,u=n.get(d.a2.id)??d.a2;return l===d.a1&&u===d.a2?d:{...d,a1:l,a2:u}}),r=new Map;for(let d of o)r.set(d.id,d);let s=e.chains.map(d=>{let l=d.backboneAtoms.map(c=>n.get(c.id)??c),u=d.bonds.map(c=>r.get(c.id)??c);return {id:d.id,polymerType:d.polymerType,backboneAtoms:l,bonds:u,...d.annotation!==void 0?{annotation:d.annotation}:{}}});return {atoms:e.atoms.map(d=>n.get(d.id)??d),bonds:o,chains:s,groups:e.groups,annotations:e.annotations}}_friendlyBondError(e,t,n,o,r){return e.includes(\"duplicate bond\")?`bond ${t.symbol}:R${o} \\u2194 ${n.symbol}:R${r} already exists`:e.includes(\"does not exist\")?\"one of the endpoint atoms is missing\":e}_validateAddBondConstraints(e,t,n,o){let r=this._mol.bonds,s=be(e);if(s>0&&(n<1||n>s))throw new P(\"rgroup-not-on-monomer\",`R-group R${n} is not defined on monomer '${e.symbol}' (has R1..R${s})`,{atomId:e.id,requested:n,total:s});let a=be(t);if(a>0&&(o<1||o>a))throw new P(\"rgroup-not-on-monomer\",`R-group R${o} is not defined on monomer '${t.symbol}' (has R1..R${a})`,{atomId:t.id,requested:o,total:a});if(s>0){let d=Ot(e,r).find(l=>l.rNumber===n);if(d!==void 0){let l=d.side===\"r1\"?d.bond.a2:d.bond.a1;throw new P(\"rgroup-already-bonded\",`R-group R${n} on '${e.symbol}' is already bonded to '${l.symbol}' (${l.bio.chainId}:${l.bio.positionInChain})`,{atomId:e.id,requested:n,conflictingBondId:d.bond.id})}}if(a>0){let d=Ot(t,r).find(l=>l.rNumber===o);if(d!==void 0){let l=d.side===\"r1\"?d.bond.a2:d.bond.a1;throw new P(\"rgroup-already-bonded\",`R-group R${o} on '${t.symbol}' is already bonded to '${l.symbol}' (${l.bio.chainId}:${l.bio.positionInChain})`,{atomId:t.id,requested:o,conflictingBondId:d.bond.id})}}for(let d of r){if(d.r1.kind!==\"numeric\"||d.r2.kind!==\"numeric\")continue;let l=d.a1.id===e.id&&d.a2.id===t.id&&d.r1.r===n&&d.r2.r===o,u=d.a1.id===t.id&&d.a2.id===e.id&&d.r1.r===o&&d.r2.r===n;if(l||u)throw new P(\"duplicate-bond\",`bond ${e.symbol}:R${n} \\u2194 ${t.symbol}:R${o} already exists`,{atomId:e.id,bondId:d.id})}}_freeRgroupsOn(e){return W(e,this._mol.bonds)}addHydrogenBond(e,t){this._ensureLive();let n=new N(this._mol),o={kind:\"pair\"},r=n.addBond({a1:e.id,a2:t.id,kind:\"hbond\",r1:o,r2:o}),{mol:s}=n.commit();this._replaceMol(s,\"addHydrogenBond\",\"api\");let a=xt(s,r);if(a===void 0)throw new Error(\"HelmEditor.addHydrogenBond: lost bond after commit\");return this._events.fire(\"bond:add\",{bond:a,source:\"api\"}),a}removeBond(e){this._ensureLive();let t=typeof e==\"number\"?e:e.id,n=xt(this._mol,t);if(n===void 0)return;let o=new N(this._mol);o.removeBond(t);let{mol:r}=o.commit();this._replaceMol(r,\"removeBond\",\"api\"),this._events.fire(\"bond:remove\",{bond:n,source:\"api\"});}replaceMonomer(e,t){this._ensureLive();let n=J(this._mol,e.id);if(n===void 0)return;let o=n.symbol;if(o===t)return;let r=new N(this._mol);r.updateAtom(e.id,{symbol:t});let{mol:s}=r.commit(),a=ke(s,this._service.monomerLib,{mode:\"lenient\"}).mol;this._replaceMol(a,`replaceMonomer:${o}->${t}`,\"api\");let d=J(a,e.id);d!==void 0&&this._events.fire(\"monomer:replace\",{atom:d,oldSymbol:o,newSymbol:t});}hitTest(e,t){this._ensureLive();let o=new q(this._mol,this._theme).test({x:e,y:t});return o===null?null:o.atom!==void 0?{atom:o.atom}:o.bond!==void 0?{bond:o.bond}:null}moveAtom(e,t){this._ensureLive();let n=J(this._mol,e);if(n===void 0||n.p.x===t.x&&n.p.y===t.y)return;let o=new N(this._mol);o.updateAtom(e,{p:{x:t.x,y:t.y}});let{mol:r}=o.commit();this._replaceMol(r,\"moveAtom\",\"user\");}moveAtoms(e){if(this._ensureLive(),e.length===0)return;let t=new N(this._mol),n=0;for(let r of e){let s=J(this._mol,r.atomId);s!==void 0&&(s.p.x===r.p.x&&s.p.y===r.p.y||(t.updateAtom(r.atomId,{p:{x:r.p.x,y:r.p.y}}),n+=1));}if(n===0)return;let{mol:o}=t.commit();this._replaceMol(o,\"moveAtom\",\"user\");}cleanLayout(e){this._ensureLive(),this._resetLastAction();let t=oe(this._mol,this._options.bondLength!==void 0?{bondLength:this._options.bondLength}:void 0);this._mol=t,this._history.push({mol:t,label:\"cleanLayout\"}),this._events.fire(\"layout:change\",{mol:t,strategy:\"auto\"}),this._events.fire(\"mol:changed\",{mol:t,changedAtomIds:new Set(t.atoms.map(n=>n.id)),changedBondIds:ge,reason:\"cleanLayout\"});}canUndo(){return this._history.canUndo()}canRedo(){return this._history.canRedo()}undo(){this._ensureLive();let e=this._history.undo();e!==null&&this._restoreFromHistory(e.mol,\"undo\");}redo(){this._ensureLive();let e=this._history.redo();e!==null&&this._restoreFromHistory(e.mol,\"redo\");}on(e,t){return this._events.on(e,t)}off(e,t){this._events.off(e,t);}fire(e,t){this._events.fire(e,t);}zoom(e,t){if(this._ensureLive(),!Number.isFinite(e)||e<=0)return;let n=this._viewport.scale,o=Math.min(Ha,Math.max(Pa,n*e));if(o===n)return;let r={...this._viewport.offset},s=r;t!==void 0&&(s={x:r.x+(n-o)*t.x,y:r.y+(n-o)*t.y});let a={scale:o,offset:s};this._viewport=a;let d=t??{x:0,y:0};this._events.fire(\"view:zoom\",{scale:o,center:d,previousScale:n}),this._events.fire(\"view:viewport-change\",{viewport:a});}panTo(e){this._ensureLive();let t={...this._viewport.offset},n={scale:this._viewport.scale,offset:{...e}};this._viewport=n,this._events.fire(\"view:pan\",{offset:n.offset,previousOffset:t}),this._events.fire(\"view:viewport-change\",{viewport:n});}getViewport(){return {scale:this._viewport.scale,offset:{...this._viewport.offset}}}fitToContent(e){this._ensureLive();let t=0,n=0,o=0,r=0,s=false;for(let c of this._mol.atoms){if(!s){t=o=c.p.x,n=r=c.p.y,s=true;continue}c.p.x<t&&(t=c.p.x),c.p.x>o&&(o=c.p.x),c.p.y<n&&(n=c.p.y),c.p.y>r&&(r=c.p.y);}let a=s?{x:t,y:n,width:o-t,height:r-n}:{x:0,y:0,width:0,height:0},d={...this._viewport.offset},l=this._viewport.scale,u={scale:1,offset:{x:0,y:0}};this._viewport=u,l!==1&&this._events.fire(\"view:zoom\",{scale:1,center:{x:0,y:0},previousScale:l}),(d.x!==0||d.y!==0)&&this._events.fire(\"view:pan\",{offset:u.offset,previousOffset:d}),this._events.fire(\"view:viewport-change\",{viewport:u}),this._events.fire(\"view:fit-to-content\",{bbox:a});}setViewOnly(e){this._ensureLive();let t=this._viewOnly;t!==e&&(this._viewOnly=e,this._events.fire(\"option:change\",{key:\"viewOnly\",oldValue:t,newValue:e}));}setTheme(e){this._ensureLive();let t=this._theme;t!==e&&(this._theme=e,this._events.fire(\"theme:change\",{theme:e,previousTheme:t}));}toSvg(e){this._ensureLive();let t=this.getHelm(),n={};return e?.width!==void 0&&(n.width=e.width),e?.height!==void 0&&(n.height=e.height),this._service.renderToSvg(t,n)}async toPng(e){this._ensureLive();let t=this.getHelm(),n={};return e?.width!==void 0&&(n.width=e.width),e?.height!==void 0&&(n.height=e.height),this._service.renderToPng(t,n)}_getHost(){return this._host}_observerCount(){return this._events.observerCount()}_currentHighlights(){return this._highlights}_currentTheme(){return this._theme}_getView(){return this._view}_getViewport(){return this._viewport}openAtomProps(e){this._ensureLive(),this._host!==null&&(this._atomDialog===null&&(this._atomDialog=new We(this)),this._atomDialog.open(e));}openBondProps(e){this._ensureLive(),this._host!==null&&(this._bondDialog===null&&(this._bondDialog=new je(this)),this._bondDialog.open(e));}openFindReplace(){this._ensureLive(),this._host!==null&&(this._findReplaceDialog===null&&(this._findReplaceDialog=new qe(this)),this._findReplaceDialog.open());}getMode(){return this._mode}setMode(e){this._ensureLive();let t=this._mode;t!==e&&(this._mode=e,this._events.fire(\"option:change\",{key:\"mode\",oldValue:t,newValue:e}));}getNextAddSymbol(){return this._nextAdd}setNextAddSymbol(e,t){this._ensureLive();let n=this._nextAdd;if(e===null)this._nextAdd=null;else {if(t===void 0)return;this._nextAdd={symbol:e,biotype:t};}this._events.fire(\"option:change\",{key:\"nextAdd\",oldValue:n,newValue:this._nextAdd});}startPaletteDrag(e,t){if(this._ensureLive(),this._dnd===null){this._events.fire(\"dnd:start\",{source:\"palette\",symbol:e});return}this._dnd.startPaletteDrag(e,t);}findMonomers(e){this._ensureLive();let t=[];for(let n of this._mol.atoms)n.symbol===e&&t.push(n);return t}replaceMonomers(e,t){this._ensureLive();let n,o;if(typeof e==\"string\"){let l=e,u=t;if(n=this.findMonomers(l),n.length===0)return 0;if(l===u)return n.length;o=`${l}->${u}`;}else {let l=t,u=new Set,c=[];for(let m of e){if(u.has(m.id))continue;u.add(m.id);let p=J(this._mol,m.id);p!==void 0&&p.symbol!==l&&c.push(p);}if(c.length===0)return 0;n=c,o=`atoms[${c.length}]->${l}`;}let r=t,s=new N(this._mol);for(let l of n)s.updateAtom(l.id,{symbol:r});let{mol:a}=s.commit(),d=ke(a,this._service.monomerLib,{mode:\"lenient\"}).mol;return this._replaceMol(d,`replaceMonomers:${o}`,\"api\"),n.length}nudgeSelection(e,t){this._ensureLive();let n=this._selection;if(n.atoms.size===0)return;let o=new N(this._mol);for(let s of n.atoms){let a=J(this._mol,s);a!==void 0&&o.updateAtom(s,{p:{x:a.p.x+e,y:a.p.y+t}});}let{mol:r}=o.commit();this._replaceMol(r,\"nudge\",\"user\");}deleteSelection(){this._ensureLive();let e=this._selection;if(e.atoms.size===0&&e.bonds.size===0)return;let t=new N(this._mol);for(let o of e.atoms)t.removeAtom(o);for(let o of e.bonds)t.removeBond(o);let{mol:n}=t.commit();this._selection=V.empty(),this._replaceMol(n,\"delete-selection\",\"user\"),this._events.fire(\"selection:change\",{selection:this._selection,addedAtomIds:ge,removedAtomIds:e.atoms,addedBondIds:ge,removedBondIds:e.bonds});}appendRnaTriplet(e,t,n){this._ensureLive();let o=Ye(e,t,n),r=this.getHelm(),s=Da(r,o);this.setHelm(s);}placeRnaTriplet(e,t,n){this._ensureLive();let o=1.6*(this._options.bondLength??28),r,s=this._mol.atoms;if(this._lastAction===\"add-triplet\"&&this._lastTripletSugarPos!==null)r={x:this._lastTripletSugarPos.x+o*2,y:this._lastTripletSugarPos.y};else if(s.length===0)r={x:0,y:0};else {let A=s[0].p.x,w=s[0].p.y;for(let k of s)k.p.x<A&&(A=k.p.x),k.p.y>w&&(w=k.p.y);r={x:A,y:w+o};}let a={x:r.x+o,y:r.y},d={x:r.x,y:r.y+o},l=new Set;for(let A of this._mol.chains)l.add(A.id);let u=1;for(;l.has(`RNA${u}`);)u+=1;let c=`RNA${u}`,m=new N(this._mol),p=m.addAtom({p:r,biotype:g.SUGAR,symbol:e,chainId:c,positionInChain:1}),h=m.addAtom({p:a,biotype:g.LINKER,symbol:n,chainId:c,positionInChain:2}),y=m.addAtom({p:d,biotype:g.BASE,symbol:t,chainId:c,positionInChain:0});m.addBond({a1:p,a2:y,kind:\"branch\",r1:{kind:\"numeric\",r:3},r2:{kind:\"numeric\",r:1}}),m.addBond({a1:p,a2:h,kind:\"backbone\",r1:{kind:\"numeric\",r:2},r2:{kind:\"numeric\",r:1}});let{mol:f}=m.commit(),_=this._postProcessTripletMol(f,p,y,c),b=ke(_,this._service.monomerLib,{mode:\"lenient\"}).mol;this._replaceMol(b,\"placeRnaTriplet\",\"user\"),this._lastAction=\"add-triplet\",this._lastTripletSugarPos=r;}_postProcessTripletMol(e,t,n,o){let r=new Map,s=J(e,n),a=J(e,t);if(s===void 0||a===void 0)return e;let d={...a,branchAtom:s};r.set(t,d);let l=e.bonds.map(h=>{let y=r.get(h.a1.id)??h.a1,f=r.get(h.a2.id)??h.a2;return y===h.a1&&f===h.a2?h:{...h,a1:y,a2:f}}),u=new Map;for(let h of l)u.set(h.id,h);let c=e.chains.map(h=>{let y=[];for(let _ of h.backboneAtoms)h.id===o&&_.id===n||y.push(r.get(_.id)??_);let f=h.bonds.map(_=>u.get(_.id)??_);return {id:h.id,polymerType:h.polymerType,backboneAtoms:y,bonds:f,...h.annotation!==void 0?{annotation:h.annotation}:{}}}),p={atoms:e.atoms.map(h=>r.get(h.id)??h),bonds:l,chains:c,groups:e.groups,annotations:e.annotations};return p=this._refreshContinuousIdsLocal(p),p}_resetLastAction(){this._lastAction=\"other\",this._lastTripletSugarPos=null;}_ensureLive(){if(this._destroyed)throw new Error(\"HelmEditor: this instance has been destroyed.\")}_replaceMol(e,t,n){let o=this._service.serialize(this._mol),r=this._service.serialize(e);this._mol=e,this._history.push({mol:e,label:t}),this._resetLastAction(),this._events.fire(\"mol:changed\",{mol:e,changedAtomIds:new Set(e.atoms.map(s=>s.id)),changedBondIds:new Set(e.bonds.map(s=>s.id)),reason:t}),o!==r&&this._events.fire(\"helm:changed\",{helm:r,mol:e,source:n});}_restoreFromHistory(e,t){let n=this._service.serialize(this._mol),o=this._service.serialize(e);this._mol=e,this._resetLastAction(),this._events.fire(\"mol:changed\",{mol:e,changedAtomIds:new Set(e.atoms.map(r=>r.id)),changedBondIds:new Set(e.bonds.map(r=>r.id)),reason:t}),n!==o&&this._events.fire(\"helm:changed\",{helm:o,mol:e,source:t});}};function Un(i){return i.startsWith(\"[\")&&i.endsWith(\"]\")||i.length===1&&/^[A-Za-z]$/.test(i)?i:`[${i}]`}function Ye(i,e,t){return `${Un(i)}(${Un(e)})${Un(t)}`}function Da(i,e){if(i===\"\")return `RNA1{${e}}$$$$V2.0`;let t=/(^|\\|)(RNA\\d+)\\{([^}]*)\\}/g,n=null,o;for(;(o=t.exec(i))!==null;)n={name:o[2],body:o[3],matchText:o[0]};if(n!==null){let h=n.body===\"\"?\"\":\".\",y=`${n.matchText.startsWith(\"|\")?\"|\":\"\"}${n.name}{${n.body}${h}${e}}`,f=i.lastIndexOf(n.matchText);return i.slice(0,f)+y+i.slice(f+n.matchText.length)}let r=new Set,s=/RNA(\\d+)\\{/g,a;for(;(a=s.exec(i))!==null;)r.add(Number(a[1]));let d=1;for(;r.has(d);)d+=1;let l=`RNA${d}{${e}}`,u=i.indexOf(\"$\");if(u<0)return `${i}|${l}$$$$V2.0`;let c=i.slice(0,u),m=i.slice(u);return `${c}${c===\"\"?\"\":\"|\"}${l}${m}`}var Oa=5,Na=3,Fa=14,Ga=11,Va=9,Ua=8,za=48,Ka=96;function Wa(i){return i<=Na?Fa:i<=6?Ga:i<=9?Va:Ua}function Hi(i,e){let t=D(e.monomer,e.biotype,e.theme.colorTheme),n=At(t.background),o=t.text,r=ro(o,n)<Oa,s=e.monomer.symbol,a=Wa(s.length),l=s.length>=10?\"line-height:1.1;letter-spacing:-0.02em;\":\"\",u=`font-size:${a}px;${l}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:${Ka-16}px;display:inline-block;`,c=v(i,\"span\",{class:\"hw-palette__star\"},[e.favorite?\"\\u2605\":\"\\u2606\"]),m=v(i,\"span\",{class:\"hw-palette__label\",style:u},[s]),p=[\"hw-palette__tile\"];e.primed&&p.push(\"hw-palette__tile--primed\"),e.favorite&&p.push(\"hw-palette__tile--favorite\"),r&&p.push(\"hw-palette__tile--low-contrast\");let h=e.monomer.name!==void 0?`${s} \\u2014 ${e.monomer.name}`:s,y=`background:${n};color:${o};width:100%;min-width:${za}px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return {root:v(i,\"div\",{class:p.join(\" \"),draggable:\"true\",role:\"button\",\"aria-pressed\":e.primed?\"true\":\"false\",\"aria-label\":h,\"data-symbol\":s,\"data-biotype\":e.biotype,\"data-bg\":n,\"data-raw-bg\":t.background,\"data-testid\":`palette-tile-${s}`,title:h,style:y},[c,m]),star:c}}function $i(i,e){let t=e.showStar!==false,n=v(i,\"span\",{class:\"hw-triplet-chip__star\"},[e.favorite?\"\\u2605\":\"\\u2606\"]),o=v(i,\"span\",{class:\"hw-triplet-chip__label\"},[e.label]),r=[\"hw-triplet-chip\"];e.favorite&&r.push(\"hw-triplet-chip--favorite\");let s=t?[n,o]:[o];return {root:v(i,\"div\",{class:r.join(\" \"),role:\"button\",tabindex:\"0\",\"aria-label\":e.title,\"data-sugar\":e.sugar,\"data-base\":e.base,\"data-linker\":e.linker,\"data-triplet\":e.label,\"data-testid\":`palette-triplet-${e.label}`,title:e.title,style:`background:${e.background};color:${e.textColor};`},s),star:n}}var ce=\"http://www.w3.org/2000/svg\",Di={sugar:g.SUGAR,base:g.BASE,linker:g.LINKER},ja={sugar:[\"r\",\"R\"],base:[\"A\"],linker:[\"p\",\"P\"]},qa=200,Ya=180,lt={x:70,y:60},zn={x:140,y:60},Kn={x:70,y:130},Xe=18,Oi=18,dt=22,Yt=class Yt{constructor(e,t,n){this.onValueSet=new Z;this.onPickModeChange=new Z;this._slots=new Map;this._favStar=null;this._pickMode=null;this._destroyed=false;this._builderRdkitCache=new Map;this._editor=t,this._doc=n?.documentImpl??S(e),this._hooks=n?.paletteHooks??null,this._favHooks=n?.favoriteHooks??null,this.element=v(this._doc,\"div\",{class:\"hw-rna-builder\",\"data-testid\":\"rna-builder\"});let o=v(this._doc,\"div\",{class:\"hw-rna-builder__header\"});if(o.appendChild(v(this._doc,\"div\",{class:\"hw-rna-builder__title\"},[\"RNA builder\"])),this._favHooks!==null){let d=v(this._doc,\"span\",{class:\"hw-rna-builder__fav hw-rna-builder__fav--disabled\",role:\"button\",tabindex:\"0\",\"data-testid\":\"rna-builder-fav-star\",title:\"Favorite this triplet\",\"aria-pressed\":\"false\",\"aria-disabled\":\"true\"},[\"\\u2606\"]),l=u=>{u.stopPropagation();let c=this.getSelection();c.preview===\"\"||this._favHooks===null||this._favHooks.toggleFavoriteTriplet(c.sugar,c.base,c.linker);};d.addEventListener(\"click\",l),d.addEventListener(\"keydown\",u=>{let c=u;(c.key===\"Enter\"||c.key===\" \")&&l(u);}),this._favStar=d,o.appendChild(d);}this.element.appendChild(o),this._hintEl=v(this._doc,\"div\",{class:\"hw-rna-builder__hint\",\"data-testid\":\"rna-builder-hint\",hidden:true}),this.element.appendChild(this._hintEl);let r=this._buildSvg();this.element.appendChild(r),this._preview=v(this._doc,\"div\",{class:\"hw-rna-builder__preview\",\"data-testid\":\"rna-builder-preview\"}),this.element.appendChild(this._preview),this._addBtn=v(this._doc,\"button\",{class:\"hw-rna-builder__add\",type:\"button\",\"data-testid\":\"rna-builder-add-btn\"},[\"Add triplet\"]),this._addBtn.addEventListener(\"click\",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),e.appendChild(this.element);let s=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh();}),a=t.on(\"theme:change\",()=>{this._destroyed||this._repaintSlotColors();});this._libUnsub=()=>{try{s();}catch{}try{a();}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors();}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors();}getSelection(){let e=this._slots.get(\"sugar\")?.value??\"\",t=this._slots.get(\"base\")?.value??\"\",n=this._slots.get(\"linker\")?.value??\"\",o=e!==\"\"&&t!==\"\"&&n!==\"\"?Ye(e,t,n):\"\";return {sugar:e,base:t,linker:n,preview:o}}setField(e,t){let n=this._slots.get(e);n!==void 0&&(n.value=t,this._setLabelText(n.labelEl,t),this._repaintSlot(n),this._updatePreview(),this.onValueSet.next({field:e,symbol:t}));}startPickMode(e){if(this._pickMode===e){this.cancelPickMode();return}this._pickMode!==null&&this._setSlotPressed(this._pickMode,false),this._pickMode=e,this._setSlotPressed(e,true),this._setHintActive(e),this.onPickModeChange.next({field:e}),this._hooks!==null&&this._hooks.beginBiotypeFilter(Di[e],t=>{this.setField(e,t),this._exitPickMode();},()=>{this._exitPickMode();});}cancelPickMode(){this._pickMode!==null&&(this._hooks!==null&&this._hooks.endBiotypeFilter(),this._exitPickMode());}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked();}destroy(){this._destroyed||(this._destroyed=true,this._pickMode!==null&&this._hooks!==null&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element));}_buildSvg(){let e=this._doc.createElementNS(ce,\"svg\");e.setAttribute(\"class\",\"hw-rna-builder__triplet\"),e.setAttribute(\"viewBox\",`0 0 ${qa} ${Ya}`),e.setAttribute(\"data-testid\",\"rna-builder-triplet-svg\"),e.setAttribute(\"role\",\"group\"),e.setAttribute(\"aria-label\",\"Triplet preview\");let t=this._doc.createElementNS(ce,\"line\");t.setAttribute(\"class\",\"hw-rna-builder__bond\"),t.setAttribute(\"x1\",String(lt.x+Xe)),t.setAttribute(\"y1\",String(lt.y)),t.setAttribute(\"x2\",String(zn.x-Oi)),t.setAttribute(\"y2\",String(zn.y)),e.appendChild(t);let n=this._doc.createElementNS(ce,\"line\");n.setAttribute(\"class\",\"hw-rna-builder__bond\"),n.setAttribute(\"x1\",String(lt.x)),n.setAttribute(\"y1\",String(lt.y+Xe)),n.setAttribute(\"x2\",String(Kn.x)),n.setAttribute(\"y2\",String(Kn.y-dt)),e.appendChild(n);let o=this._doc.createElementNS(ce,\"rect\");o.setAttribute(\"class\",\"hw-rna-builder__slot-shape\"),o.setAttribute(\"x\",String(-Xe)),o.setAttribute(\"y\",String(-Xe)),o.setAttribute(\"width\",String(Xe*2)),o.setAttribute(\"height\",String(Xe*2)),o.setAttribute(\"rx\",\"8\"),o.setAttribute(\"ry\",\"8\");let r=this._buildSlot(\"sugar\",\"Pick sugar (backbone)\",lt,o),s=this._doc.createElementNS(ce,\"circle\");s.setAttribute(\"class\",\"hw-rna-builder__slot-shape\"),s.setAttribute(\"cx\",\"0\"),s.setAttribute(\"cy\",\"0\"),s.setAttribute(\"r\",String(Oi));let a=this._buildSlot(\"linker\",\"Pick linker\",zn,s),d=this._doc.createElementNS(ce,\"path\");d.setAttribute(\"class\",\"hw-rna-builder__slot-shape\"),d.setAttribute(\"d\",`M ${-dt} 0 L 0 ${-dt} L ${dt} 0 L 0 ${dt} Z`);let l=this._buildSlot(\"base\",\"Pick base\",Kn,d);return e.appendChild(a.groupEl),e.appendChild(r.groupEl),e.appendChild(l.groupEl),this._slots.set(\"sugar\",r),this._slots.set(\"linker\",a),this._slots.set(\"base\",l),e}_buildSlot(e,t,n,o){let r=this._doc.createElementNS(ce,\"g\");r.setAttribute(\"class\",\"hw-rna-builder__slot\"),r.setAttribute(\"data-slot\",e),r.setAttribute(\"data-testid\",`rna-builder-slot-${e}`),r.setAttribute(\"role\",\"button\"),r.setAttribute(\"tabindex\",\"0\"),r.setAttribute(\"aria-label\",t),r.setAttribute(\"aria-pressed\",\"false\"),r.setAttribute(\"transform\",`translate(${n.x} ${n.y})`),r.appendChild(o);let s=this._doc.createElementNS(ce,\"text\");s.setAttribute(\"class\",\"hw-rna-builder__slot-label\"),s.setAttribute(\"data-testid\",`rna-builder-${e}-value`),s.setAttribute(\"x\",\"0\"),s.setAttribute(\"y\",\"0\"),s.setAttribute(\"text-anchor\",\"middle\"),s.setAttribute(\"dominant-baseline\",\"central\"),r.appendChild(s);let a=d=>{d.stopPropagation(),this.startPickMode(e);};return r.addEventListener(\"click\",a),r.addEventListener(\"keydown\",d=>{let l=d;(l.key===\"Enter\"||l.key===\" \")&&a(d);}),r.addEventListener(\"mouseenter\",d=>this._showSlotTooltip(e,d)),r.addEventListener(\"mouseleave\",()=>this._hideSlotTooltip()),r.addEventListener(\"focus\",()=>this._showSlotTooltip(e,null)),r.addEventListener(\"blur\",()=>this._hideSlotTooltip()),{id:e,biotype:Di[e],groupEl:r,shapeEl:o,labelEl:s,value:\"\"}}_setLabelText(e,t){let n=[];for(let a=e.firstChild;a!==null;a=a.nextSibling)a.nodeName===\"title\"||a.nodeName===\"TITLE\"||n.push(a);for(let a of n)e.removeChild(a);let o=Xa(t);e.setAttribute(\"font-size\",String(o)),e.setAttribute(\"text-anchor\",\"middle\"),e.setAttribute(\"dominant-baseline\",\"central\");let r=t.length>10?`${t.slice(0,9)}\\u2026`:t;e.appendChild(this._doc.createTextNode(r));let s=e.parentNode;if(s!==null){let a=null;for(let d=s.firstChild;d!==null;d=d.nextSibling)if(d.nodeName===\"title\"||d.nodeName===\"TITLE\"){a=d;break}for(a===null&&(a=this._doc.createElementNS(ce,\"title\"),s.insertBefore(a,s.firstChild));a.firstChild!==null;)a.removeChild(a.firstChild);a.appendChild(this._doc.createTextNode(t));}}_repaintSlotColors(){for(let e of this._slots.values())this._repaintSlot(e);}_repaintSlot(e){let t=this._editor.getService().monomerLib,n=this._theme(),o=e.value===\"\"?null:Qa(t,e.biotype,e.value),r=D(o,e.biotype,n.colorTheme);e.shapeEl.style.fill=r.background,e.shapeEl.style.stroke=r.line,e.labelEl.style.fill=r.text;}_populateDefaults(){let e=this._editor.getService().monomerLib;for(let[t,n]of this._slots.entries()){let o=Ja(e,n.biotype),r=Za(o,ja[t]),s=n.value!==\"\"&&o.some(a=>a.symbol===n.value)?n.value:r??o[0]?.symbol??\"\";n.value=s,this._setLabelText(n.labelEl,s);}}_updatePreview(){let e=this.getSelection();for(;this._preview.firstChild!==null;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(e.preview===\"\"?\"-\":e.preview)),this._updateFavStar(e);}_updateFavStar(e){if(this._favStar===null||this._favHooks===null)return;let t=e.preview!==\"\",n=t&&this._favHooks.isFavoriteTriplet(e.sugar,e.base,e.linker);for(;this._favStar.firstChild!==null;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(n?\"\\u2605\":\"\\u2606\")),this._favStar.setAttribute(\"aria-pressed\",n?\"true\":\"false\"),t?this._favStar.removeAttribute(\"aria-disabled\"):this._favStar.setAttribute(\"aria-disabled\",\"true\");let o=\"hw-rna-builder__fav\"+(n?\" hw-rna-builder__fav--active\":\"\")+(t?\"\":\" hw-rna-builder__fav--disabled\");this._favStar.setAttribute(\"class\",o);}_onAddClicked(){let e=this.getSelection();e.preview!==\"\"&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker);}_exitPickMode(){if(this._pickMode===null)return;let e=this._pickMode;this._setSlotPressed(e,false),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null});}_setHintActive(e){let t=this._hintEl;for(;t.firstChild!==null;)t.removeChild(t.firstChild);if(e===null){t.setAttribute(\"hidden\",\"\");return}t.removeAttribute(\"hidden\");let n=e===\"sugar\"?\"sugar\":e===\"base\"?\"base\":\"linker\";t.appendChild(this._doc.createTextNode(`Pick ${n} from palette`));}_setSlotPressed(e,t){let n=this._slots.get(e);if(n===void 0)return;n.groupEl.setAttribute(\"aria-pressed\",t?\"true\":\"false\");let r=(n.groupEl.getAttribute(\"class\")??\"\").split(/\\s+/).filter(s=>s!==\"hw-rna-builder__slot--active\").join(\" \");n.groupEl.setAttribute(\"class\",t?`${r} hw-rna-builder__slot--active`:r);}_theme(){let e=this._editor;return typeof e._currentTheme==\"function\"?e._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(e===null)return null;let t=e.smiles;if(t===void 0||t===\"\")return null;let n=this._rdkit();if(n===null)return null;let o=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(o))return this._builderRdkitCache.get(o)??null;let r=ye(n,t,220,140);if(this._builderRdkitCache.size>=Yt._BUILDER_RDKIT_CACHE_LIMIT){let s=this._builderRdkitCache.keys().next().value;s!==void 0&&this._builderRdkitCache.delete(s);}return this._builderRdkitCache.set(o,r),r}_slotHint(e){switch(e){case \"sugar\":return \"Click to choose a different sugar\";case \"base\":return \"Click to choose a different base\";case \"linker\":return \"Click to choose a different linker\"}}_slotTitle(e,t){let n=t===\"\"?\"?\":t;switch(e){case \"sugar\":return `Sugar: ${n}`;case \"base\":return `Base: ${n}`;case \"linker\":return `Linker: ${n}`}}_showSlotTooltip(e,t){let n=this._slots.get(e);if(n===void 0)return;let r=this._editor.getService().monomerLib.getMonomerSet(n.biotype),s=n.value===\"\"?null:r.get(n.value)??null,a=ie(this._doc,\"builder-tooltip\",\"hw-builder-tooltip\");Te(this._doc,a,{symbol:this._slotTitle(e,n.value),name:s?.name??\"\",rdkitSvg:this._builderRdkitSvgFor(s),rdkitTestid:\"builder-tooltip-rdkit-svg\",hint:this._slotHint(e)});let d=t;if(d!==null&&typeof d.clientX==\"number\"&&typeof d.clientY==\"number\")Y(a,d.clientX,d.clientY);else {let l=n.groupEl,u=typeof l.getBoundingClientRect==\"function\"?l.getBoundingClientRect():null;u!==null?Y(a,u.left+u.width/2,u.top+u.height/2):Y(a,0,0);}}_hideSlotTooltip(){let e=this._doc.body.querySelector('[data-testid=\"builder-tooltip\"]');U(e);}};Yt._BUILDER_RDKIT_CACHE_LIMIT=256;var qt=Yt;function Xa(i){let e=i.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}function Ja(i,e){let t=i.getMonomerSet(e),n=[];for(let o of t.values())n.push(o);return n.sort((o,r)=>o.symbol.localeCompare(r.symbol)),n}function Za(i,e){let t=new Set;for(let n of i)t.add(n.symbol);for(let n of e)if(t.has(n))return n;return null}function Qa(i,e,t){return i.getMonomerSet(e).get(t)??null}var ue=\"Favorites\",Wn={[ue]:\"\\u2605 Favorites\",[x.PEPTIDE]:\"Peptides\",[x.RNA]:\"RNA\",[x.CHEM]:\"CHEM\",[x.BLOB]:\"BLOB\",G:\"G\"},Xt=[ue,x.PEPTIDE,x.RNA,x.CHEM,x.BLOB,\"G\"],Ni=\"hwe:palette:favorites\",Fi=\"hwe:palette:active-tab\",el=\"hwe.palette.favorites\";function Jt(i){return `${i.sugar}|${i.base}|${i.linker}`}var Je=class Je{constructor(e,t,n){this.favoritesChanged=new Z;this._nextAddUnsub=()=>{};this._favorites=new Set;this._favoriteTriplets=[];this._pendingRnaSelection=null;this._visibleTabs=[ue];this._activeTab=ue;this._searchInput=null;this._filter=\"\";this._destroyed=false;this._rnaBuilder=null;this._activeBiotypeFilter=null;this._pickResolver=null;this._pickCanceller=null;this._pickEscapeListener=null;this._pickOutsideClickListener=null;this._paletteRdkitCache=new Map;this._editor=t,this._doc=n?.documentImpl??S(e),this._opts={documentImpl:this._doc,groupByNaturalAnalog:n?.groupByNaturalAnalog??true,allowFavorites:n?.allowFavorites??true},this._loadFavorites(),this._activeTab=this._resolveInitialTab(n?.initialTab),this.element=v(this._doc,\"div\",{class:\"hw-palette\",\"data-testid\":\"palette\"}),e.appendChild(this.element),this._render(),this._libUnsub=t.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh();}),this._themeUnsub=t.on(\"theme:change\",()=>{this._destroyed||this.refresh();}),this._nextAddUnsub=t.on(\"option:change\",o=>{this._destroyed||o.key===\"nextAdd\"&&this._updatePrimedClasses();});}refresh(){this._render();}setFilter(e){this._filter=e.trim().toLowerCase(),this._searchInput!==null&&this._searchInput.value!==e&&(this._searchInput.value=e),this._applyFilter();}setActiveTab(e){this._visibleTabs.includes(e)&&(this._activeTab=e,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter());}getActiveTab(){return this._activeTab}getFavorites(){let e=this._editor.getService().monomerLib,t=[];for(let n of this._favorites)this._findMonomer(e,n)!==null&&t.push(n);return t}setFavorite(e,t){let n=this._favorites.has(e);t!==n&&(t?this._favorites.add(e):this._favorites.delete(e),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged());}clearFavorites(){this._favorites.size===0&&this._favoriteTriplets.length===0||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged());}getFavoriteTriplets(){return this._favoriteTriplets.map(e=>({...e}))}isFavoriteTriplet(e,t,n){let o=Jt({sugar:e,base:t,linker:n});return this._favoriteTriplets.some(r=>Jt(r)===o)}setFavoriteTriplet(e,t,n,o){let r=Jt({sugar:e,base:t,linker:n}),s=this._favoriteTriplets.findIndex(d=>Jt(d)===r),a=s>=0;o!==a&&(o?this._favoriteTriplets.push({sugar:e,base:t,linker:n}):this._favoriteTriplets.splice(s,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged());}_hidePaletteTooltips(){let e=this._doc.body;U(e.querySelector('[data-testid=\"palette-tooltip\"]')),U(e.querySelector('[data-testid=\"palette-triplet-tooltip\"]'));}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()});}destroy(){this._destroyed||(this._destroyed=true,this._rnaBuilder!==null&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element));}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return this._activeBiotypeFilter!==null}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(this._activeBiotypeFilter===null)return;let e=this._pickCanceller;this._teardownPickMode(),e?.();}_buildPaletteFilterHooks(){return {beginBiotypeFilter:(e,t,n)=>{this._activeBiotypeFilter!==null&&this._teardownPickMode(),this._activeBiotypeFilter=e,this._pickResolver=t,this._pickCanceller=n,this._applyFilter();let o=d=>{d.key===\"Escape\"&&this.cancelBiotypeFilter();};this._pickEscapeListener=o,this._doc.defaultView?.addEventListener(\"keydown\",o);let s=d=>{if(this._activeBiotypeFilter===null)return;let l=d.target;if(l==null)return;let u=this._activeBiotypeFilter,c=l;for(;c!==null;){let m=c.getAttribute===void 0?null:c.getAttribute(\"class\");if(m!==null){let p=m.split(/\\s+/);if(p.includes(\"hw-palette__tile\")){if((c.getAttribute(\"data-biotype\")??\"\")===u)return;break}if(p.includes(\"hw-rna-builder__slot\")){if(this._isInsideOwnPalette(c))return;break}}c=c.parentElement;}this.cancelBiotypeFilter();};this._pickOutsideClickListener=s,this._doc.addEventListener(\"mousedown\",s,true);},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let e=this.element.querySelector(`.hw-palette__pane[data-tab=\"${this._activeTab}\"]`);if(e===null)return;let t=e;try{if(typeof t.scrollTo==\"function\"){t.scrollTo({top:0,behavior:\"smooth\"});return}}catch{}typeof t.scrollTop==\"number\"&&(t.scrollTop=0);}_isInsideOwnPalette(e){let t=e;for(;t!==null;){if(t===this.element)return  true;t=t.parentElement;}return  false}_teardownPickMode(){this._activeBiotypeFilter!==null&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener!==null&&(this._doc.defaultView?.removeEventListener(\"keydown\",this._pickEscapeListener),this._pickEscapeListener=null),this._pickOutsideClickListener!==null&&(this._doc.removeEventListener(\"mousedown\",this._pickOutsideClickListener,true),this._pickOutsideClickListener=null),this._applyFilter());}_render(){for(this._rnaBuilder!==null&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);this.element.firstChild!==null;)this.element.removeChild(this.element.firstChild);let e=this._doc.createElement(\"input\");e.setAttribute(\"type\",\"search\"),e.setAttribute(\"class\",\"hw-palette__search\"),e.setAttribute(\"placeholder\",\"Search monomers...\"),e.setAttribute(\"data-testid\",\"palette-search\"),this._filter!==\"\"&&(e.value=this._filter),e.addEventListener(\"input\",()=>this.setFilter(e.value)),this._searchInput=e,this.element.appendChild(e),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=ue);let t=v(this._doc,\"div\",{class:\"hw-palette__tabs\",role:\"tablist\",\"data-testid\":\"palette-tabs\"});for(let s of this._visibleTabs){let a=s===this._activeTab,d=v(this._doc,\"button\",{class:\"hw-palette__tab\",type:\"button\",role:\"tab\",\"aria-controls\":`hw-palette-pane-${s}`,\"aria-selected\":a?\"true\":\"false\",\"data-testid\":`palette-tab-${s}`,\"data-tab\":s,title:Wn[s]},[Wn[s]]);d.addEventListener(\"click\",()=>this.setActiveTab(s)),t.appendChild(d);}this.element.appendChild(t);let n=v(this._doc,\"div\",{class:\"hw-palette__panes\"}),o=this._theme(),r=this._editor.getService().monomerLib;for(let s of this._visibleTabs){let a=s===this._activeTab,d=v(this._doc,\"div\",{class:\"hw-palette__pane\",id:`hw-palette-pane-${s}`,role:\"tabpanel\",\"data-testid\":`palette-pane-${s}`,\"data-tab\":s,hidden:!a});s===ue?this._buildFavoritesPane(d,r,o):this._buildPolymerPane(d,s,r,o),n.appendChild(d);}this.element.appendChild(n),this._applyFilter();}_computeVisibleTabs(){let e=this._editor.getService().monomerLib,t=new Set;for(let o of e.getPolymerTypes())t.add(o);let n=[];n.push(ue);for(let o of Xt)o!==ue&&t.has(o)&&n.push(o);return n}_buildFavoritesPane(e,t,n){let o=this._resolveFavoriteMonomers(t),r=this._favoriteTriplets;if(o.length===0&&r.length===0){let s=v(this._doc,\"div\",{class:\"hw-palette__placeholder\",\"data-testid\":\"palette-favorites-empty\"},[\"No favorites yet \\u2014 click the \\u2606 on any tile to add one.\"]);e.appendChild(s);return}for(let[s,a]of this._groupByPolymerAndType(o))e.appendChild(this._renderGroup(s,a));r.length>0&&e.appendChild(this._renderTripletGroup(\"RNA \\xB7 Triplets\",r,t));}_groupByPolymerAndType(e){let t=new Map;for(let s of e){let a=s.polymerType,d=s.monomerType??\"Undefined\",l=`${a}|${d}`,u=t.get(l);u===void 0&&(u={pt:a,mt:d,list:[]},t.set(l,u)),u.list.push(s);}let n=s=>{let a=Xt.indexOf(s);return a<0?99:a},o={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(t.values()).sort((s,a)=>n(s.pt)-n(a.pt)||(o[s.mt]??9)-(o[a.mt]??9)||s.mt.localeCompare(a.mt)).map(s=>[`${this._polymerLabel(s.pt)} \\xB7 ${s.mt}`,s.list])}_polymerLabel(e){return Wn[e]??e}_renderTripletGroup(e,t,n){let o=v(this._doc,\"div\",{class:\"hw-palette__group\",\"data-natural-analog\":e}),r=v(this._doc,\"div\",{class:\"hw-palette__group-header\",\"data-testid\":`palette-group-${e}`},[e]),s=v(this._doc,\"div\",{class:\"hw-triplet-chips\",\"data-testid\":\"palette-triplet-favorites\"});for(let a of t)s.appendChild(this._renderTripletChip(a,n));return o.appendChild(r),o.appendChild(s),o}_renderTripletChip(e,t){let n=Ye(e.sugar,e.base,e.linker),o=t.getMonomerSet(g.BASE).get(e.base)??null,r=D(o,g.BASE,this._theme().colorTheme),s=this.isFavoriteTriplet(e.sugar,e.base,e.linker),a=o?.name!==void 0&&o.name!==\"\"?`${n} \\u2014 ${o.name}`:n,{root:d}=$i(this._doc,{sugar:e.sugar,base:e.base,linker:e.linker,label:n,title:a,background:At(r.background),textColor:r.text,favorite:s,showStar:this._opts.allowFavorites});return this._wireTripletChip(d,e),d}_wireTripletChip(e,t){e.addEventListener(\"mouseenter\",n=>{let o=n,r=ie(this._doc,\"palette-triplet-tooltip\",\"hw-palette-tooltip hw-triplet-tooltip\");xi(this._doc,r,{title:Ye(t.sugar,t.base,t.linker),parts:this._tripletTooltipParts(t),hint:\"Click to add this triplet\",rdkitTestid:\"palette-triplet-tooltip-rdkit-svg\"}),Y(r,typeof o.clientX==\"number\"?o.clientX:0,typeof o.clientY==\"number\"?o.clientY:0);}),e.addEventListener(\"mouseleave\",()=>{U(this._doc.body.querySelector('[data-testid=\"palette-triplet-tooltip\"]'));}),e.addEventListener(\"click\",n=>{let o=n.target;if(this._opts.allowFavorites&&o?.classList?.contains(\"hw-triplet-chip__star\")===true){this.setFavoriteTriplet(t.sugar,t.base,t.linker,!this.isFavoriteTriplet(t.sugar,t.base,t.linker)),n.stopPropagation();return}this._editor.placeRnaTriplet(t.sugar,t.base,t.linker);}),e.addEventListener(\"keydown\",n=>{let o=n;(o.key===\"Enter\"||o.key===\" \")&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker);});}_buildRnaDefaultChips(e){let t=this._pickSymbol(e.getMonomerSet(g.SUGAR),[\"r\",\"R\"]),n=this._pickSymbol(e.getMonomerSet(g.LINKER),[\"p\",\"P\"]),o=e.getMonomerSet(g.BASE);if(t===null||n===null)return null;let r=Je._DEFAULT_TRIPLET_BASES.filter(a=>o.has(a));if(r.length===0)return null;let s=v(this._doc,\"div\",{class:\"hw-triplet-chips hw-triplet-chips--defaults\",\"data-testid\":\"rna-default-triplets\"});for(let a of r)s.appendChild(this._renderTripletChip({sugar:t,base:a,linker:n},e));return s}_tripletTooltipParts(e){let t=this._editor.getService().monomerLib,n=(o,r,s)=>{let a=t.getMonomerSet(r).get(s)??null;return {role:o,symbol:s,...a?.name!==void 0?{name:a.name}:{},rdkitSvg:a===null?null:this._paletteRdkitSvg(a)}};return [n(\"Sugar\",g.SUGAR,e.sugar),n(\"Base\",g.BASE,e.base),n(\"Linker\",g.LINKER,e.linker)]}_pickSymbol(e,t){for(let o of t)if(e.has(o))return o;let n=e.keys().next();return n.done===true?null:n.value}_restoreRnaSelection(){let e=this._pendingRnaSelection;if(this._pendingRnaSelection=null,e===null||this._rnaBuilder===null)return;let t=this._editor.getService().monomerLib;e.sugar!==\"\"&&t.getMonomerSet(g.SUGAR).has(e.sugar)&&this._rnaBuilder.setField(\"sugar\",e.sugar),e.base!==\"\"&&t.getMonomerSet(g.BASE).has(e.base)&&this._rnaBuilder.setField(\"base\",e.base),e.linker!==\"\"&&t.getMonomerSet(g.LINKER).has(e.linker)&&this._rnaBuilder.setField(\"linker\",e.linker);}_resolveFavoriteMonomers(e){let t=[];for(let n of this._favorites){let o=this._findMonomer(e,n);o!==null&&t.push(o);}return t}_findMonomer(e,t){for(let n of e.getPolymerTypes()){let o=e.getMonomer(n,t);if(o!==null)return o}return null}_buildPolymerPane(e,t,n,o){let r=t,s=this._monomersForPolymer(r,n);if(s.length===0)return;if(r===x.RNA){this._rnaBuilder=new qt(e,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(m,p,h)=>this.isFavoriteTriplet(m,p,h),toggleFavoriteTriplet:(m,p,h)=>this.setFavoriteTriplet(m,p,h,!this.isFavoriteTriplet(m,p,h))}:null}),this._restoreRnaSelection();let u=this._buildRnaDefaultChips(n);u!==null&&e.appendChild(u);let c=this._groupRna(s);for(let[m,p]of c)p.length!==0&&e.appendChild(this._renderGroup(m,p));return}if(r===x.PEPTIDE&&this._opts.groupByNaturalAnalog){let u=this._groupByAnalog(s);for(let[c,m]of u){let p=c===\"\"?\"Other\":c;e.appendChild(this._renderGroup(p,m));}return}let a=v(this._doc,\"div\",{class:\"hw-palette__group-tiles\"}),d=this._editor.getNextAddSymbol(),l=this._sortByColor(s);for(let u of l){let c=this._biotype(u,r);a.appendChild(this._renderTile(u,c,d));}e.appendChild(a);}_renderGroup(e,t){let n=v(this._doc,\"div\",{class:\"hw-palette__group\",\"data-natural-analog\":e}),o=v(this._doc,\"div\",{class:\"hw-palette__group-header\",\"data-testid\":`palette-group-${e}`},[e]),r=v(this._doc,\"div\",{class:\"hw-palette__group-tiles\"}),s=this._editor.getNextAddSymbol(),a=this._sortByColor(t);for(let d of a){let l=this._biotype(d,d.polymerType);r.appendChild(this._renderTile(d,l,s));}return n.appendChild(o),n.appendChild(r),n}_sortByColor(e){let t=this._theme(),n=e.map((o,r)=>{let s=this._biotype(o,o.polymerType),a=D(o,s,t.colorTheme),d=so(a.background),l=d.s===0?1:0;return {m:o,idx:r,h:d.h,s:d.s,l:d.l,isGrey:l}});return n.sort((o,r)=>o.isGrey!==r.isGrey?o.isGrey-r.isGrey:o.h!==r.h?o.h-r.h:o.s!==r.s?o.s-r.s:o.l!==r.l?o.l-r.l:o.idx-r.idx),n.map(o=>o.m)}_monomersForPolymer(e,t){let n=t.getMonomerSymbolsByType(e),o=[];for(let r of n){let s=t.getMonomer(e,r);s!==null&&o.push(s);}return o.sort((r,s)=>r.symbol.localeCompare(s.symbol)),o}_groupByAnalog(e){let t=new Map;for(let r of e){let s=r.naturalAnalog??\"\",a=t.get(s);a===void 0&&(a=[],t.set(s,a)),a.push(r);}let n=[],o=Array.from(t.keys()).sort((r,s)=>r===\"\"&&s!==\"\"?1:s===\"\"&&r!==\"\"?-1:r.localeCompare(s));for(let r of o)n.push([r,t.get(r)]);return new Map(n)}_groupRna(e){let t=[],n=[],o=[],r=[];for(let a of e){let d=te(a);d===g.SUGAR?t.push(a):d===g.BASE?n.push(a):d===g.LINKER?o.push(a):r.push(a);}let s=new Map;return s.set(\"Backbones\",t),s.set(\"Bases\",n),s.set(\"Linkers\",o),r.length>0&&s.set(\"Other\",r),s}_renderTile(e,t,n){let o=this._favorites.has(e.symbol),r=n!==null&&n.symbol===e.symbol&&n.biotype===t,{root:s,star:a}=Hi(this._doc,{monomer:e,biotype:t,theme:this._theme(),favorite:o,primed:r});return this._wireTile(s,a,e,t),s}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let t=e.smiles;if(t===void 0||t===\"\")return null;let n=this._rdkit();if(n===null)return null;let o=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(o))return this._paletteRdkitCache.get(o)??null;let r=ye(n,t,220,140);if(this._paletteRdkitCache.size>=Je._PALETTE_RDKIT_CACHE_LIMIT){let s=this._paletteRdkitCache.keys().next().value;s!==void 0&&this._paletteRdkitCache.delete(s);}return this._paletteRdkitCache.set(o,r),r}_wireTile(e,t,n,o){e.addEventListener(\"mouseenter\",r=>{let s=r,a=ie(this._doc,\"palette-tooltip\",\"hw-palette-tooltip\");Te(this._doc,a,{symbol:n.symbol,name:n.name??\"\",rdkitSvg:this._paletteRdkitSvg(n),rdkitTestid:\"palette-tooltip-rdkit-svg\"});let d=typeof s.clientX==\"number\"?s.clientX:0,l=typeof s.clientY==\"number\"?s.clientY:0;Y(a,d,l);}),e.addEventListener(\"mouseleave\",()=>{U(this._doc.body.querySelector('[data-testid=\"palette-tooltip\"]'));}),e.addEventListener(\"click\",r=>{let s=r.target;if(this._opts.allowFavorites&&s!==void 0&&s?.classList?.contains(\"hw-palette__star\")===true){this.setFavorite(n.symbol,!this._favorites.has(n.symbol)),r.stopPropagation();return}if(this._activeBiotypeFilter!==null&&this._activeBiotypeFilter===o){let l=this._pickResolver;this._teardownPickMode(),l?.(n.symbol),this._scrollActivePaneToTop(),r.stopPropagation();return}let a=this._editor.getSelection();if(a.atoms.size>0){let l=this._editor.getMol(),u=[];for(let m of a.atoms){let p=l.atoms.find(h=>h.id===m);p!==void 0&&u.push(p);}if(u.length>0&&u.every(m=>m.biotype===o)){this._editor.replaceMonomers(u,n.symbol),r.stopPropagation();return}this._editor.fire(\"editor:status\",{message:`Cannot bulk-replace ${u.length} selected atom(s) with ${n.symbol}: selection contains incompatible biotypes for ${o}.`,severity:\"warn\",durationMs:3e3}),r.stopPropagation();return}let d=this._editor.getNextAddSymbol();if(d!==null&&d.symbol===n.symbol&&d.biotype===o){this._editor.setNextAddSymbol(null),this._updatePrimedClasses();return}this._editor.setNextAddSymbol(n.symbol,o),this._updatePrimedClasses();}),e.addEventListener(\"dragstart\",r=>{let s=r.dataTransfer;if(s!=null)try{s.setData(\"application/x-hwe-monomer\",JSON.stringify({symbol:n.symbol,biotype:o})),s.effectAllowed=\"copy\";}catch{}U(this._doc.body.querySelector('[data-testid=\"palette-tooltip\"]')),this._editor.startPaletteDrag(n.symbol,o);});}_biotype(e,t){let n=te(e);if(n!==null)return n;switch(t){case x.PEPTIDE:return g.AA;case x.RNA:return g.SUGAR;case x.CHEM:return g.CHEM;case x.BLOB:return g.BLOB;default:return g.CHEM}}_theme(){let e=this._editor;return typeof e._currentTheme==\"function\"?e._currentTheme():this._editor.getService().theme}_applyFilter(){let e=this._filter,t=this._activeBiotypeFilter,n=this.element.querySelector(`.hw-palette__pane[data-tab=\"${this._activeTab}\"]`),o=(n??this.element).querySelectorAll(\".hw-palette__tile\");for(let a=0;a<o.length;a++){let d=o[a],l=(d.getAttribute(\"data-symbol\")??\"\").toLowerCase(),u=(d.getAttribute(\"title\")??\"\").toLowerCase(),c=d.getAttribute(\"data-biotype\")??\"\",h=(e===\"\"||l.indexOf(e)>=0||u.indexOf(e)>=0)&&(t===null||c===t);d.style.display=h?\"\":\"none\";}let r=(n??this.element).querySelectorAll(\".hw-triplet-chip\");for(let a=0;a<r.length;a++){let d=r[a],l=[d.getAttribute(\"data-triplet\")??\"\",d.getAttribute(\"data-sugar\")??\"\",d.getAttribute(\"data-base\")??\"\",d.getAttribute(\"data-linker\")??\"\"].join(\" \").toLowerCase(),u=(e===\"\"||l.indexOf(e)>=0)&&t===null;d.style.display=u?\"\":\"none\";}let s=(n??this.element).querySelectorAll(\".hw-palette__group\");for(let a=0;a<s.length;a++){let d=s[a],l=d.querySelectorAll(\".hw-palette__tile, .hw-triplet-chip\"),u=false;for(let c=0;c<l.length;c++)if(l[c].style.display!==\"none\"){u=true;break}u?(d.removeAttribute(\"hidden\"),d.removeAttribute(\"data-section-empty\")):(d.setAttribute(\"hidden\",\"\"),d.setAttribute(\"data-section-empty\",\"true\"));}}_updatePrimedClasses(){let e=this._editor.getNextAddSymbol(),t=this.element.querySelectorAll(\".hw-palette__tile\");for(let n=0;n<t.length;n++){let o=t[n],r=o.getAttribute(\"data-symbol\")??\"\",s=o.getAttribute(\"data-biotype\")??\"\",a=e!==null&&e.symbol===r&&e.biotype===s,l=(o.getAttribute(\"class\")??\"\").split(/\\s+/).filter(u=>u!==\"hw-palette__tile--primed\").join(\" \");o.setAttribute(\"class\",a?`${l} hw-palette__tile--primed`:l),o.setAttribute(\"aria-pressed\",a?\"true\":\"false\");}}_applyActiveTabClasses(){let e=this.element.querySelectorAll(\".hw-palette__tab\");for(let n=0;n<e.length;n++){let o=e[n],r=o.getAttribute(\"data-tab\")??\"\";o.setAttribute(\"aria-selected\",r===this._activeTab?\"true\":\"false\");}let t=this.element.querySelectorAll(\".hw-palette__pane\");for(let n=0;n<t.length;n++){let o=t[n];(o.getAttribute(\"data-tab\")??\"\")===this._activeTab?o.removeAttribute(\"hidden\"):o.setAttribute(\"hidden\",\"\");}}_localStorage(){if(!this._opts.allowFavorites)return null;let e=this._doc.defaultView;if(e==null)return null;try{return e.localStorage??null}catch{return null}}_resolveInitialTab(e){if(e!==void 0&&Xt.includes(e))return e;let t=this._localStorage();if(t!==null)try{let n=t.getItem(Fi);if(n!==null&&Xt.includes(n))return n}catch{}return ue}_persistActiveTab(){let e=this._localStorage();if(e!==null)try{e.setItem(Fi,this._activeTab);}catch{}}_loadFavorites(){let e=this._localStorage();if(e!==null){try{let t=e.getItem(Ni);if(t!==null&&t!==\"\"){let n=JSON.parse(t),o=this._extractSymbols(n);for(let r of o)this._favorites.add(r);for(let r of this._extractTriplets(n))this._favoriteTriplets.push(r);return}}catch{}try{let t=e.getItem(el);if(t===null||t===\"\")return;let n=JSON.parse(t);if(Array.isArray(n)){for(let o of n){if(typeof o!=\"string\")continue;let r=o.indexOf(\"|\"),s=r>=0?o.slice(r+1):o;s!==\"\"&&this._favorites.add(s);}this._saveFavorites();}}catch{}}}_extractSymbols(e){if(Array.isArray(e)){let t=[];for(let n of e)typeof n==\"string\"&&t.push(n);return t}if(e!==null&&typeof e==\"object\"){let t=e;if(Array.isArray(t.symbols)){let n=[];for(let o of t.symbols)typeof o==\"string\"&&n.push(o);return n}}return []}_extractTriplets(e){if(e===null||typeof e!=\"object\")return [];let t=e;if(!Array.isArray(t.triplets))return [];let n=[];for(let o of t.triplets){if(o===null||typeof o!=\"object\")continue;let r=o;typeof r.sugar==\"string\"&&typeof r.base==\"string\"&&typeof r.linker==\"string\"&&n.push({sugar:r.sugar,base:r.base,linker:r.linker});}return n}_saveFavorites(){let e=this._localStorage();if(e!==null)try{let t={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(t.triplets=this._favoriteTriplets.map(n=>({...n}))),e.setItem(Ni,JSON.stringify(t));}catch{}}};Je._DEFAULT_TRIPLET_BASES=[\"A\",\"C\",\"G\",\"U\",\"T\"],Je._PALETTE_RDKIT_CACHE_LIMIT=256;var ct=Je;var z='<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"1.5\" stroke-linecap=\"round\" stroke-linejoin=\"round\">',tl={new:`${z}<path d=\"M13 3H7a2 2 0 0 0-2 2v14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V9z\"/><path d=\"M13 3v6h6\"/><line x1=\"12\" y1=\"12.5\" x2=\"12\" y2=\"17.5\"/><line x1=\"9.5\" y1=\"15\" x2=\"14.5\" y2=\"15\"/></svg>`,open:`${z}<path d=\"m6 14 1.45-2.9A2 2 0 0 1 9.24 10H20a2 2 0 0 1 1.94 2.5l-1.55 6a2 2 0 0 1-1.94 1.5H4a2 2 0 0 1-2-2V5a2 2 0 0 1 2-2h3.93a2 2 0 0 1 1.66.9l.82 1.2a2 2 0 0 0 1.66.9H18a2 2 0 0 1 2 2v2\"/></svg>`,save:`${z}<rect x=\"8\" y=\"2\" width=\"8\" height=\"4\" rx=\"1\" ry=\"1\"/><path d=\"M16 4h2a2 2 0 0 1 2 2v14a2 2 0 0 1-2 2H6a2 2 0 0 1-2-2V6a2 2 0 0 1 2-2h2\"/><path d=\"m9 14 2 2 4-4\"/></svg>`,undo:`${z}<path d=\"M3 12a9 9 0 1 0 9-9 9.7 9.7 0 0 0-6.7 2.8L3 8\"/><path d=\"M3 3v5h5\"/></svg>`,redo:`${z}<path d=\"M21 12a9 9 0 1 1-9-9 9.7 9.7 0 0 1 6.7 2.8L21 8\"/><path d=\"M21 3v5h-5\"/></svg>`,eraser:`${z}<path d=\"m7 21-4.3-4.3c-1-1-1-2.5 0-3.4l9.6-9.6c1-1 2.5-1 3.4 0l5.6 5.6c1 1 1 2.5 0 3.4L13 21\"/><path d=\"M22 21H7\"/><path d=\"m5 11 9 9\"/></svg>`,select:`${z}<path d=\"m4 4 7.07 17 2.51-7.39L21 11.07z\"/></svg>`,hbond:`${z}<path d=\"M9 17H7A5 5 0 0 1 7 7h2\"/><path d=\"M15 7h2a5 5 0 1 1 0 10h-2\"/><line x1=\"8\" y1=\"12\" x2=\"16\" y2=\"12\"/></svg>`,\"zoom-in\":`${z}<circle cx=\"11\" cy=\"11\" r=\"8\"/><line x1=\"21\" y1=\"21\" x2=\"16.65\" y2=\"16.65\"/><line x1=\"11\" y1=\"8\" x2=\"11\" y2=\"14\"/><line x1=\"8\" y1=\"11\" x2=\"14\" y2=\"11\"/></svg>`,\"zoom-out\":`${z}<circle cx=\"11\" cy=\"11\" r=\"8\"/><line x1=\"21\" y1=\"21\" x2=\"16.65\" y2=\"16.65\"/><line x1=\"8\" y1=\"11\" x2=\"14\" y2=\"11\"/></svg>`,fit:`${z}<polyline points=\"15 3 21 3 21 9\"/><polyline points=\"9 21 3 21 3 15\"/><line x1=\"21\" y1=\"3\" x2=\"14\" y2=\"10\"/><line x1=\"3\" y1=\"21\" x2=\"10\" y2=\"14\"/></svg>`,move:`${z}<polyline points=\"5 9 2 12 5 15\"/><polyline points=\"9 5 12 2 15 5\"/><polyline points=\"15 19 12 22 9 19\"/><polyline points=\"19 9 22 12 19 15\"/><line x1=\"2\" y1=\"12\" x2=\"22\" y2=\"12\"/><line x1=\"12\" y1=\"2\" x2=\"12\" y2=\"22\"/></svg>`,clean:`${z}<path d=\"m21.64 3.64-1.28-1.28a1.21 1.21 0 0 0-1.72 0L2.36 18.64a1.21 1.21 0 0 0 0 1.72l1.28 1.28a1.2 1.2 0 0 0 1.72 0L21.64 5.36a1.2 1.2 0 0 0 0-1.72Z\"/><path d=\"m14 7 3 3\"/><path d=\"M5 6v4\"/><path d=\"M19 14v4\"/><path d=\"M10 2v2\"/><path d=\"M7 8H3\"/><path d=\"M21 16h-4\"/><path d=\"M11 3H9\"/></svg>`,find:`${z}<circle cx=\"11\" cy=\"11\" r=\"8\"/><line x1=\"21\" y1=\"21\" x2=\"16.65\" y2=\"16.65\"/></svg>`,theme:`${z}<circle cx=\"12\" cy=\"12\" r=\"9\"/><path d=\"M12 3a9 9 0 0 1 0 18z\" fill=\"currentColor\" stroke=\"none\"/></svg>`},nl={new:\"New \\u2014 clear the canvas\",open:\"Open \\u2014 paste a HELM string\",save:\"Save \\u2014 copy HELM string to clipboard\",undo:\"Undo last action\",redo:\"Redo last undone action\",eraser:\"Eraser \\u2014 click an atom or bond to delete it\",select:\"Select mode (default)\",hbond:\"H-Bond mode \\u2014 drag between two RNA bases to add a Watson-Crick pair\",\"zoom-in\":\"Zoom in\",\"zoom-out\":\"Zoom out\",fit:\"Fit to content \\u2014 reset zoom and pan\",move:\"Move/Pan mode \\u2014 drag the canvas to scroll\",clean:\"Clean layout \\u2014 re-run automatic layout\",find:\"Find / Replace monomer\",theme:\"Toggle dark / light theme\"},Gi=[{id:\"new\",label:\"New\",icon:\"New\"},{id:\"open\",label:\"Open\",icon:\"Open\"},{id:\"save\",label:\"Save\",icon:\"Save\"},{id:\"undo\",label:\"Undo\",icon:\"\\u21BA\",shortcut:\"Ctrl+Z\",separator:true},{id:\"redo\",label:\"Redo\",icon:\"\\u21BB\",shortcut:\"Ctrl+Y\"},{id:\"eraser\",label:\"Eraser\",icon:\"Eraser\",separator:true},{id:\"select\",label:\"Select\",icon:\"Select\"},{id:\"hbond\",label:\"H-Bond\",icon:\"H-Bond\"},{id:\"zoom-in\",label:\"Zoom In\",icon:\"+\",shortcut:\"Ctrl++\",separator:true},{id:\"zoom-out\",label:\"Zoom Out\",icon:\"\\u2212\",shortcut:\"Ctrl+\\u2212\"},{id:\"fit\",label:\"Fit\",icon:\"Fit\",shortcut:\"0\"},{id:\"move\",label:\"Move\",icon:\"Move\"},{id:\"clean\",label:\"Clean\",icon:\"Clean\",separator:true},{id:\"find\",label:\"Find\",icon:\"Find\",shortcut:\"Ctrl+F\"},{id:\"theme\",label:\"Theme\",icon:\"Theme\",separator:true}],ut=class{constructor(e,t,n){this._buttons=new Map;this._unsubs=[];this._destroyed=false;this._editor=t,this._doc=n?.documentImpl??S(e);let o=n?.buttons??Gi;this.element=v(this._doc,\"div\",{class:\"hw-toolbar\",\"data-testid\":\"toolbar\"}),e.appendChild(this.element);for(let s of o){if(s.separator===true){let d=v(this._doc,\"span\",{class:\"hw-toolbar__separator\"});this.element.appendChild(d);}let a=this._buildButton(s);this.element.appendChild(a),this._buttons.set(s.id,a);}let r=()=>this._refreshHistoryState();this._unsubs.push(t.on(\"mol:changed\",r)),this._unsubs.push(t.on(\"helm:changed\",r)),r(),this._reflectMode(),this._unsubs.push(t.on(\"option:change\",s=>{s.key===\"mode\"&&this._reflectMode();}));}setButtonEnabled(e,t){let n=this._buttons.get(e);n!==void 0&&(t?n.removeAttribute(\"disabled\"):n.setAttribute(\"disabled\",\"\"));}destroy(){if(!this._destroyed){this._destroyed=true,this._hideTip();for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_buildButton(e){let t=this._doc.createElement(\"button\");t.setAttribute(\"class\",\"hw-toolbar__btn\"),t.setAttribute(\"type\",\"button\"),t.setAttribute(\"data-action\",e.id),t.setAttribute(\"data-testid\",`toolbar-${e.id}`);let n=nl[e.id]??e.label,o=e.shortcut!==void 0?`${n}  (${e.shortcut})`:n;t.setAttribute(\"data-tooltip\",o),t.setAttribute(\"aria-label\",n),t.addEventListener(\"mouseenter\",s=>{let a=s;this._showTip(o,typeof a.clientX==\"number\"?a.clientX:0,typeof a.clientY==\"number\"?a.clientY:0);}),t.addEventListener(\"mouseleave\",()=>this._hideTip()),t.addEventListener(\"click\",()=>this._hideTip());let r=tl[e.id];if(r!==void 0){let s=this._doc.createElement(\"span\");s.setAttribute(\"class\",\"hw-toolbar__btn-icon\"),s.setAttribute(\"aria-hidden\",\"true\"),s.innerHTML=r,t.appendChild(s);}else {let s=e.icon??e.label;t.appendChild(this._doc.createTextNode(s));}return t.addEventListener(\"click\",()=>this._invoke(e.id)),t}_showTip(e,t,n){let o=ie(this._doc,\"toolbar-tooltip\",\"hw-toolbar-tooltip\");for(;o.firstChild!==null;)o.removeChild(o.firstChild);o.appendChild(this._doc.createTextNode(e)),Y(o,t,n);}_hideTip(){U(this._doc.body.querySelector('[data-testid=\"toolbar-tooltip\"]'));}_invoke(e){let t=false;this._editor.fire(\"key:command\",{command:e,preventDefault:()=>{t=true;}}),!t&&this._execute(e);}_execute(e){switch(e){case \"new\":this._editor.setHelm(\"\");return;case \"open\":{let t=this._doc.defaultView;if(t!=null&&typeof t.prompt==\"function\"){let n=t.prompt(\"Enter HELM string\");n!==null&&this._editor.setHelm(n);}return}case \"save\":{let t=this._editor.getHelm();this._editor.fire(\"clipboard:copy\",{format:\"helm\",payload:t});return}case \"undo\":this._editor.undo();return;case \"redo\":this._editor.redo();return;case \"eraser\":{if(!this._editor.getSelection().isEmpty){this._editor.deleteSelection();return}this._editor.setMode(\"eraser\");return}case \"select\":case \"hbond\":case \"move\":this._editor.setMode(e);return;case \"zoom-in\":this._editor.zoom(1.1,this._molCenterOrUndefined());return;case \"zoom-out\":this._editor.zoom(1/1.1,this._molCenterOrUndefined());return;case \"fit\":this._editor.fitToContent();return;case \"clean\":this._editor.cleanLayout();return;case \"find\":this._editor.openFindReplace();return;case \"theme\":{let t=this._editor,n=typeof t._currentTheme==\"function\"?t._currentTheme():null,o=n!==null&&n.name===\"dark\";this._editor.setTheme(o?$:In);return}default:return}}_refreshHistoryState(){this.setButtonEnabled(\"undo\",this._editor.canUndo()),this.setButtonEnabled(\"redo\",this._editor.canRedo());}_molCenterOrUndefined(){let e=this._editor.getMol();if(e.atoms.length===0)return;let t=e.atoms[0].p.x,n=t,o=e.atoms[0].p.y,r=o;for(let s=1;s<e.atoms.length;s++){let a=e.atoms[s].p;a.x<t&&(t=a.x),a.x>n&&(n=a.x),a.y<o&&(o=a.y),a.y>r&&(r=a.y);}return {x:(t+n)/2,y:(o+r)/2}}_reflectMode(){let e=this._editor.getMode();for(let t of [\"select\",\"eraser\",\"hbond\",\"move\"]){let n=this._buttons.get(t);if(n===void 0)continue;let r=(n.getAttribute(\"class\")??\"\").split(/\\s+/).filter(s=>s!==\"hw-toolbar__btn--active\").join(\" \");n.setAttribute(\"class\",t===e?`${r} hw-toolbar__btn--active`:r);}}};var mt=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._editor=t,this._doc=n?.documentImpl??S(e),this._content=v(this._doc,\"pre\",{class:\"hw-pane__content hw-pane__sequence\",\"data-testid\":\"sequence-pane-content\"}),this.element=v(this._doc,\"div\",{class:\"hw-pane hw-pane--sequence\",\"data-testid\":\"pane-sequence\"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on(\"helm:changed\",()=>this.refresh())),this._unsubs.push(t.on(\"mol:changed\",()=>this.refresh()));}refresh(){if(this._destroyed)return;let e=this._compute();for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_compute(){let e=this._editor.getMol(),t=[],n;for(let o of e.atoms){let r=o.bio.chainId;n!==void 0&&r!==n&&t.push(\"|\"),n=r;let s=o.monomer?.naturalAnalog;t.push(s!==void 0&&s!==\"\"?s:o.symbol);}return t.join(\"\")}};var pt=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._suppressNext=false;this._editor=t,this._doc=n?.documentImpl??S(e),this._input=v(this._doc,\"div\",{class:\"hw-pane__content hw-pane__notation\",contenteditable:\"true\",spellcheck:\"false\",\"data-testid\":\"notation-pane-content\"}),this._error=v(this._doc,\"div\",{class:\"hw-pane__error\",\"data-testid\":\"notation-pane-error\"}),this.element=v(this._doc,\"div\",{class:\"hw-pane hw-pane--notation\",\"data-testid\":\"pane-helm\"},[this._input,this._error]),e.appendChild(this.element),this.refresh(),this._input.addEventListener(\"blur\",()=>this._commit()),this._input.addEventListener(\"keydown\",o=>{o.key===\"Enter\"&&(o.preventDefault(),o.stopPropagation(),o.stopImmediatePropagation(),this._commit());}),this._unsubs.push(t.on(\"helm:changed\",()=>{if(this._suppressNext){this._suppressNext=false;return}this.refresh();})),this._unsubs.push(t.on(\"mol:changed\",()=>this.refresh()));}refresh(){if(this._destroyed)return;let e=this._editor.getHelm();for(;this._input.firstChild!==null;)this._input.removeChild(this._input.firstChild);this._input.appendChild(this._doc.createTextNode(e)),this._clearError();}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_commit(){if(this._destroyed)return;let e=(this._input.textContent??\"\").trim(),t=this._editor.getHelm();if(e===t){this._clearError();return}let r=this._editor.getService().validate(e).filter(s=>s.severity===\"error\");if(r.length>0){this._showError(r.map(s=>s.message).join(\"; \"));return}this._clearError(),this._suppressNext=true,this._editor.setHelm(e);}_showError(e){for(;this._error.firstChild!==null;)this._error.removeChild(this._error.firstChild);this._error.appendChild(this._doc.createTextNode(e)),this._error.setAttribute(\"class\",\"hw-pane__error hw-pane__error--visible\");}_clearError(){for(;this._error.firstChild!==null;)this._error.removeChild(this._error.firstChild);this._error.setAttribute(\"class\",\"hw-pane__error\");}};var ol=1e3,ht=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._editor=t,this._doc=n?.documentImpl??S(e),this._body=v(this._doc,\"div\",{class:\"hw-pane__content hw-pane__properties\",\"data-testid\":\"properties-pane-content\"}),this.element=v(this._doc,\"div\",{class:\"hw-pane hw-pane--properties\",\"data-testid\":\"pane-properties\"},[this._body]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on(\"helm:changed\",()=>this.refresh())),this._unsubs.push(t.on(\"mol:changed\",()=>this.refresh()));}refresh(){if(this._destroyed)return;for(;this._body.firstChild!==null;)this._body.removeChild(this._body.firstChild);let e=this._editor.getHelm();if(e.length>ol){this._body.appendChild(v(this._doc,\"div\",{class:\"hw-pane__placeholder\"},[\"(too long)\"]));return}let t=this._editor.getService(),n=\"\",o=0,r=0;try{let s=t.getFormula(e);n=il(s.elements),o=s.mw;}catch{n=\"\\u2014\";}try{o=t.getMolWeight(e);}catch{}try{r=t.getExtinctionCoefficient(e);}catch{}this._body.appendChild(this._makeRow(\"Formula\",n,\"formula\")),this._body.appendChild(this._makeRow(\"Molecular Weight\",o===0?\"\\u2014\":o.toFixed(2),\"mw\")),this._body.appendChild(this._makeRow(\"Extinction Coefficient\",r===0?\"\\u2014\":r.toFixed(0),\"extinction\"));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_makeRow(e,t,n){let o=v(this._doc,\"span\",{class:\"hw-pane__prop-label\"},[e]),r=v(this._doc,\"span\",{class:\"hw-pane__prop-value\",\"data-testid\":`properties-${n}`},[t]);return v(this._doc,\"div\",{class:\"hw-pane__prop-row\"},[o,r])}};function il(i){let e=Array.from(i.keys()).sort((n,o)=>n===o?0:n===\"C\"?-1:o===\"C\"?1:n===\"H\"?-1:o===\"H\"?1:n.localeCompare(o)),t=\"\";for(let n of e){let o=i.get(n);o===void 0||o===0||(t+=o===1?n:`${n}${o}`);}return t===\"\"?\"\\u2014\":t}var ft=class{constructor(e,t,n){this._unsubs=[];this._destroyed=false;this._refreshToken=0;this._editor=t,this._doc=n?.documentImpl??S(e),this._content=v(this._doc,\"pre\",{class:\"hw-pane__content hw-pane__atomic\",\"data-testid\":\"atomic-pane-content\"}),this.element=v(this._doc,\"div\",{class:\"hw-pane hw-pane--atomic\",\"data-testid\":\"pane-atomic\"},[this._content]),e.appendChild(this.element),this.refresh(),this._unsubs.push(t.on(\"helm:changed\",()=>{this.refresh();}));}async refresh(){if(this._destroyed)return;let e=++this._refreshToken,t=this._editor.getHelm(),n=this._editor.getService();if(!n.hasAtomicMolfileProvider()){this._render(\"Atomic structure unavailable\");return}try{let o=await n.getAtomicMolfile(t);if(this._destroyed||e!==this._refreshToken)return;this._render(o);}catch(o){if(this._destroyed||e!==this._refreshToken)return;let r=o instanceof Error?o.message:String(o);this._render(`Atomic structure unavailable: ${r}`);}}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_render(e){for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e));}};function Zt(i){return i.toLowerCase().replace(/[^a-z0-9]+/g,\"-\").replace(/^-|-$/g,\"\")}var bt=class{constructor(e,t,n,o,r){this._unsubs=[];this._destroyed=false;this._active=false;this._dirty=true;this._refreshToken=0;this._editor=t,this._provider=o,this.name=n,this._doc=r?.documentImpl??S(e);let s=Zt(n);this._content=v(this._doc,\"div\",{class:\"hw-pane__content hw-pane__extra\",\"data-testid\":`extra-pane-content-${s}`}),this.element=v(this._doc,\"div\",{class:\"hw-pane hw-pane--extra\",\"data-testid\":`pane-extra-${s}`},[this._content]),e.appendChild(this.element),this._unsubs.push(t.on(\"helm:changed\",()=>{this._dirty=true,this._active&&this.refresh();}));}setActive(e){this._active=e,e&&this._dirty&&this.refresh();}async refresh(){if(this._destroyed)return;let e=++this._refreshToken;this._dirty=false;let t=this._editor.getHelm();try{let n=await this._provider(t);if(this._destroyed||e!==this._refreshToken)return;this._mount(n);}catch(n){if(this._destroyed||e!==this._refreshToken)return;let o=n instanceof Error?n.message:String(n);this._renderText(`Pane \"${this.name}\" failed: ${o}`);}}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element);}}_mount(e){for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(e);}_renderText(e){for(;this._content.firstChild!==null;)this._content.removeChild(this._content.firstChild);this._content.appendChild(this._doc.createTextNode(e));}};var rl=\"extra:\";function Qt(i){return rl+i}var sl=[{id:\"sequence\",label:\"Sequence\"},{id:\"helm\",label:\"HELM\"},{id:\"properties\",label:\"Properties\"},{id:\"atomic\",label:\"Atomic Structure\"}],yt=class{constructor(e,t){this._paneByName=new Map;this._tabsByName=new Map;this._unsubs=[];this._activePane=\"helm\";this._destroyed=false;this._statusModeNode=null;this._statusMessageNode=null;this._statusMessageTimeout=null;this._host=e,this._doc=t.documentImpl??S(e);let o=(t.theme??$).name===\"dark\"?\"hw-app hw-app--dark\":\"hw-app\";this.element=v(this._doc,\"div\",{class:o,\"data-testid\":\"app-root\"}),this._toolbarHost=v(this._doc,\"div\",{class:\"hw-app__toolbar\"}),this._paletteHost=v(this._doc,\"div\",{class:\"hw-app__palette\"}),this._canvasHost=v(this._doc,\"div\",{class:\"hw-app__canvas\",\"data-testid\":\"canvas-host\"});let r=v(this._doc,\"div\",{class:\"hw-app__main\"},[this._paletteHost,this._canvasHost]);this._tabsHost=v(this._doc,\"div\",{class:\"hw-app__tabs\",role:\"tablist\"}),this._paneBody=v(this._doc,\"div\",{class:\"hw-app__pane-body\"});let s=v(this._doc,\"div\",{class:\"hw-app__panes\"},[this._tabsHost,this._paneBody]);this.element.appendChild(this._toolbarHost),this.element.appendChild(r),this.element.appendChild(s),e.appendChild(this.element);let a={service:t.service};t.initialHelm!==void 0&&(a.initialHelm=t.initialHelm),t.width!==void 0&&(a.width=t.width),t.height!==void 0&&(a.height=t.height),this.canvas=new at(this._canvasHost,a),t.theme!==void 0&&this.canvas.setTheme(t.theme);let d={documentImpl:this._doc};t.toolbarButtons!==void 0&&(d.buttons=t.toolbarButtons),this.toolbar=new ut(this._toolbarHost,this.canvas,d),this.palette=new ct(this._paletteHost,this.canvas,{documentImpl:this._doc,...t.paletteOptions}),this.sequencePane=new mt(this._paneBody,this.canvas,{documentImpl:this._doc}),this.notationPane=new pt(this._paneBody,this.canvas,{documentImpl:this._doc}),this.propertiesPane=new ht(this._paneBody,this.canvas,{documentImpl:this._doc}),t.service.hasAtomicMolfileProvider()?this.atomicStructurePane=new ft(this._paneBody,this.canvas,{documentImpl:this._doc}):this.atomicStructurePane=null,this._paneByName.set(\"sequence\",this.sequencePane.element),this._paneByName.set(\"helm\",this.notationPane.element),this._paneByName.set(\"properties\",this.propertiesPane.element),this.atomicStructurePane!==null&&this._paneByName.set(\"atomic\",this.atomicStructurePane.element);let l=[];for(let[p,h]of t.service.getExtraPanes()){let y=new bt(this._paneBody,this.canvas,p,h,{documentImpl:this._doc});l.push(y),this._paneByName.set(Qt(p),y.element);}this.extraPanes=l;let u=this._resolveVisiblePanes(t),c=[];for(let p of u){let h=sl.find(y=>y.id===p);h!==void 0&&c.push({id:h.id,label:h.label,testid:`tab-${h.id}`});}for(let p of l)c.push({id:Qt(p.name),label:p.name,testid:`tab-extra-${Zt(p.name)}`});for(let{id:p,label:h,testid:y}of c){let f=this._doc.createElement(\"button\");f.setAttribute(\"type\",\"button\"),f.setAttribute(\"class\",\"hw-app__tab\"),f.setAttribute(\"role\",\"tab\"),f.setAttribute(\"data-pane\",p),f.setAttribute(\"data-testid\",y),f.appendChild(this._doc.createTextNode(h)),f.addEventListener(\"click\",()=>this.activatePane(p)),this._tabsHost.appendChild(f),this._tabsByName.set(p,f);}let m=u.includes(\"helm\")?\"helm\":u[0]??\"helm\";this.activatePane(m),this._unsubs.push(this.canvas.on(\"theme:change\",p=>this._applyTheme(p.theme))),this._buildStatusBar(),this._applyMode(this.canvas.getMode()),this._unsubs.push(this.canvas.on(\"option:change\",p=>{p.key===\"mode\"&&this._applyMode(p.newValue),p.key===\"nextAdd\"&&this._refreshStatus();})),this._unsubs.push(this.canvas.on(\"mol:changed\",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on(\"helm:changed\",()=>this._refreshStatus())),this._unsubs.push(this.canvas.on(\"editor:status\",p=>{this._showStatusMessage(p.message,p.severity,p.durationMs);})),this._unsubs.push(this.canvas.on(\"monomer:contextmenu\",p=>{p.preventDefault(),this.canvas.openAtomProps(p.atom);})),this._unsubs.push(this.canvas.on(\"bond:contextmenu\",p=>{p.preventDefault(),this.canvas.openBondProps(p.bond);})),this._onDocKeydown=p=>this._handleEscape(p),this._doc.addEventListener(\"keydown\",this._onDocKeydown,true);}_handleEscape(e){let t=e;t.key===\"Escape\"&&(Gt(this._doc),X.closeTopmost()&&(t.stopImmediatePropagation?.(),t.preventDefault?.()));}_buildStatusBar(){let e=v(this._doc,\"div\",{class:\"hw-status-bar\",\"data-testid\":\"status-bar\"}),t=v(this._doc,\"span\",{class:\"hw-status-bar__mode\",\"data-testid\":\"status-mode\"}),n=v(this._doc,\"span\",{class:\"hw-status-bar__message\",\"data-testid\":\"status-message\",role:\"status\",\"aria-live\":\"polite\"});e.appendChild(t),e.appendChild(n),this._canvasHost.appendChild(e),this._statusModeNode=t,this._statusMessageNode=n,this._refreshStatus();}_refreshStatus(){let e=this._statusModeNode;if(e===null)return;let t=this.canvas.getMode(),n=this.canvas.getNextAddSymbol();for(;e.firstChild!==null;)e.removeChild(e.firstChild);if(n===null){e.appendChild(this._doc.createTextNode(`Mode: ${t}  |  Next add: none`));return}e.appendChild(this._doc.createTextNode(`Mode: ${t}  |  Next add: `));let o=v(this._doc,\"span\",{class:\"hw-status-bar__next-add-symbol\",\"data-testid\":\"status-next-add-symbol\"},[n.symbol]);e.appendChild(o);let r=v(this._doc,\"button\",{type:\"button\",class:\"hw-status-bar__next-add-clear\",\"data-testid\":\"status-next-add-clear\",\"aria-label\":\"Clear next-add monomer\",title:\"Clear (Esc)\"},[\"\\xD7\"]);r.addEventListener(\"click\",s=>{s.preventDefault(),s.stopPropagation(),this.canvas.setNextAddSymbol(null);}),e.appendChild(r);}_showStatusMessage(e,t,n){let o=this._statusMessageNode;if(o!==null){for(this._statusMessageTimeout!==null&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null);o.firstChild!==null;)o.removeChild(o.firstChild);o.appendChild(this._doc.createTextNode(e)),o.setAttribute(\"data-severity\",t),n>0&&(this._statusMessageTimeout=setTimeout(()=>{let r=this._statusMessageNode;if(r!==null){for(;r.firstChild!==null;)r.removeChild(r.firstChild);r.removeAttribute(\"data-severity\"),this._statusMessageTimeout=null;}},n));}}_applyMode(e){let t=this._canvasHost.querySelector(\".hw-editor-view\");if(t===null)return;let o=(t.getAttribute(\"class\")??\"\").split(/\\s+/).filter(r=>!r.startsWith(\"hw-editor-view--\")).join(\" \");t.setAttribute(\"class\",`${o} hw-editor-view--${e}`.trim()),this._refreshStatus();}setHelm(e){this.canvas.setHelm(e);}getHelm(){return this.canvas.getHelm()}on(e,t){return this.canvas.on(e,t)}activatePane(e){if(!(!this._paneByName.has(e)&&!this._tabsByName.has(e))){this._activePane=e;for(let[t,n]of this._paneByName.entries())n.style.display=t===e?\"\":\"none\";for(let[t,n]of this._tabsByName.entries()){let r=(n.getAttribute(\"class\")??\"\").split(/\\s+/).filter(s=>s!==\"hw-app__tab--active\").join(\" \");n.setAttribute(\"class\",t===e?`${r} hw-app__tab--active`:r);}for(let t of this.extraPanes)t.setActive(this._activePane===Qt(t.name));}}getActivePane(){return this._activePane}destroy(){if(!this._destroyed){this._destroyed=true,this._statusMessageTimeout!==null&&(clearTimeout(this._statusMessageTimeout),this._statusMessageTimeout=null),this._doc.removeEventListener(\"keydown\",this._onDocKeydown,true);for(let e of this._unsubs)e();for(let e of this.extraPanes)e.destroy();this.atomicStructurePane!==null&&this.atomicStructurePane.destroy(),this.propertiesPane.destroy(),this.notationPane.destroy(),this.sequencePane.destroy(),this.palette.destroy(),this.toolbar.destroy(),this.canvas.destroy(),this.element.parentNode!==null&&this.element.parentNode.removeChild(this.element),this._host;}}_resolveVisiblePanes(e){let t=e.service.hasAtomicMolfileProvider(),n=e.visiblePanes??[\"sequence\",\"helm\",\"properties\",\"atomic\"];return t||(n=n.filter(o=>o!==\"atomic\")),n}_applyTheme(e){let t=e.name===\"dark\",o=(this.element.getAttribute(\"class\")??\"\").split(/\\s+/).filter(r=>r!==\"hw-app--dark\").join(\" \");this.element.setAttribute(\"class\",t?`${o} hw-app--dark`:o);}};var jn=class{constructor(e){this.T=\"ATOM\";this.selected=e.selected,this.highlighted=e.highlighted,this.p={x:e.p.x,y:e.p.y},this.elem=e.symbol,this.bio={type:e.biotype,continuousId:e.bio.continuousId,chainId:e.bio.chainId,positionInChain:e.bio.positionInChain,...e.bio.annotation!==void 0?{annotation:e.bio.annotation}:{},...e.bio.blobtype!==void 0?{blobtype:e.bio.blobtype}:{},...e.bio.ambiguity!==void 0?{ambiguity:e.bio.ambiguity}:{},id:e.id},e.inlineSource!==void 0&&(this.inlineSource=e.inlineSource);}biotype(){return this.bio.type}},qn=class{constructor(e,t,n){this.a1=t,this.a2=n,this.r1=Vi(e.r1),this.r2=Vi(e.r2),this.kind=e.kind;}};function Vi(i){switch(i.kind){case \"numeric\":return i.r;case \"positional\":return i.r;default:return 0}}function se(i){let e=[],t=new Map;for(let r of i.atoms){let s=new jn(r);e.push(s),t.set(r.id,s);}let n=[];for(let r of i.bonds){let s=t.get(r.a1.id),a=t.get(r.a2.id);s===void 0||a===void 0||n.push(new qn(r,s,a));}return {atoms:e,bonds:n,clone(r){return se(i)},_internalMol:i}}var al=400,ll=100,dl=14,ae=class{constructor(e,t,n){this._laidMol=null;this._currentHelm=\"\";this._drawOptions={fontsize:dl};this._noDraw=false;this._svgEl=null;this.host=e,this._service=t,this._doc=n?.documentImpl??S(e),this._width=n?.width??al,this._height=n?.height??ll,this._mol=me(),this._molView=se(this._mol),this.editor=this._buildEditor();}resizeEditor(e,t){this._width=e,this._height=t,this._redraw();}_buildEditor(){let e=this,t={get noDraw(){return e._noDraw},set noDraw(n){e._noDraw=n;},get jsd(){return e.editor}};return {get div(){return e.host},get m(){return e._molView},set m(n){e._molView=n;},get helm(){return t},get options(){return {width:e._width,height:e._height}},setData(n,o){if(o!==\"helm\")throw new Error(`LegacyEditorWrapper: only 'helm' format supported (got '${o}').`);e._setHelm(n);},setHelm(n){e._setHelm(n);},setMol(n){e._mol=n._internalMol,e._molView=e._buildView(e._mol),e._currentHelm=e._service.serialize(e._mol),e._redraw();},getHelm(n){return e._currentHelm},getMolfile(){return Dt(e._mol)},resize(n,o){e._width=n,e._height=o,e._redraw();},setSize(n,o){e._width=n,e._height=o,e._redraw();},redraw(){e._redraw();},reset(){e._mol=me(),e._laidMol=null,e._molView=se(e._mol),e._currentHelm=\"\",e._removeSvg();},getFormula(n){return cl(fe(e._mol))},getMolWeight(){return De(e._mol)},getExtinctionCoefficient(){return Oe(e._mol)},getDrawOptions(){return e._drawOptions}}}_setHelm(e){this._currentHelm=e;let t=this._service.parse(e,{mode:\"lenient\",resolveMonomers:true});this._mol=t.mol,this._molView=this._buildView(this._mol),this._redraw();}_buildView(e){return this._laidMol=this._noDraw?null:oe(e),se(this._laidMol??e)}_redraw(){if(this._noDraw){this._removeSvg();return}if(this._currentHelm===\"\"||this._laidMol===null){this._removeSvg();return}let e=new Set,t=new Set;for(let o of this._molView.atoms){let r=o.bio.id;r!==void 0&&(o.selected&&e.add(r),o.highlighted&&t.add(r));}let n=this._service.renderMolResult(this._laidMol,{width:this._width,height:this._height,maxScale:1/0,showIds:true,selectedAtomIds:e,highlightedAtomIds:t});this._bakeViewToSurface(n.bbox,n.drawBox),this._mountSvg(n.svg);}_bakeViewToSurface(e,t){if(this._laidMol===null)return;let n=t.scale,o=t.x-e.x*n,r=t.y-e.y*n,s=this._laidMol.atoms,a=this._molView.atoms,d=Math.min(s.length,a.length);for(let l=0;l<d;l++){let u=s[l].p,c=a[l].p;c.x=u.x*n+o,c.y=u.y*n+r;}}_mountSvg(e){this._removeSvg();let t=ul(this._doc,e,this._width,this._height);t.setAttribute(\"pointer-events\",\"none\"),this.host.firstChild!==null?this.host.insertBefore(t,this.host.firstChild):this.host.appendChild(t),this._svgEl=t;}_removeSvg(){this._svgEl!==null&&this._svgEl.parentNode!==null&&this._svgEl.parentNode.removeChild(this._svgEl),this._svgEl=null;}},Ui=[\"C\",\"H\",\"N\",\"O\",\"S\",\"P\"];function cl(i){let e=o=>{let r=Ui.indexOf(o);return r===-1?Ui.length:r},t=[...i.elements.keys()].sort((o,r)=>{let s=e(o),a=e(r);return s!==a?s-a:o<r?-1:o>r?1:0}),n=[];for(let o of t){let r=i.elements.get(o);n.push(r===1?o:`${o}${r}`);}return n.join(\"\")}function ul(i,e,t,n){let o=ml(i,e);if(o!==null)return o;let r=i.createElementNS(\"http://www.w3.org/2000/svg\",\"svg\");return r.setAttribute(\"width\",String(t)),r.setAttribute(\"height\",String(n)),r}function ml(i,e){let t=globalThis.DOMParser;if(t===void 0)return null;try{let r=new t().parseFromString(e,\"image/svg+xml\").documentElement;return r==null?null:i.importNode(r,!0)}catch{return null}}var pl=800,hl=400,fl=32,bl=14,Yn=class{constructor(e){this._width=0;this._height=0;this._doc=e;}resize(e,t){this._width=e,this._height=t;}select(){}dblclick(){}createMonomerDiv(e,t,n){let o=v(this._doc,\"div\",{\"data-monomer\":t,\"data-biotype\":n,\"data-testid\":`legacy-mex-monomer-${t}`});return e.appendChild(o),o}getSize(){return {width:this._width,height:this._height}}},gt=class{constructor(e,t,n){this.toolbarheight=fl;this._drawOptions={fontsize:bl};this._unsubs=[];this._destroyed=false;this._host=e,this._service=t,this._doc=n?.documentImpl??S(e),this._width=n?.width??pl,this._height=n?.height??hl;let o={service:t};n?.initialHelm!==void 0&&(o.initialHelm=n.initialHelm),n?.documentImpl!==void 0&&(o.documentImpl=n.documentImpl),n?.width!==void 0&&(o.width=n.width),n?.height!==void 0&&(o.height=n.height),this._app=new yt(e,o),this.sequence=this._app.sequencePane.element,this.notation=this._app.notationPane.element,this.properties={parent:this._app.propertiesPane.element},this._structureviewHost=v(this._doc,\"div\",{class:\"hwe-legacy-app__structureview\",\"data-testid\":\"legacy-app-structureview\"}),this._structureviewWrapper=new ae(this._structureviewHost,t,{documentImpl:this._doc}),this.structureview=this._structureviewWrapper,this.mex=new Yn(this._doc),this._editorFacade=this._buildEditorFacade();let r=this._editorFacade;this.canvas={get host(){return r.div},get editor(){return r},get helm(){return r.helm},resizeEditor:(a,d)=>{this._resize(a,d);},getHelm:a=>r.getHelm(a),setHelm:a=>{r.setHelm(a);}};let s=()=>{this._structureviewWrapper.editor.setHelm(this._app.getHelm());};this._unsubs.push(this._app.canvas.on(\"helm:changed\",s)),n?.initialHelm!==void 0&&n.initialHelm.length>0&&s();}get editorApp(){return this._app}_buildEditorFacade(){let e=this,t=this._app,n={noDraw:false,get jsd(){return e._editorFacade}};return {get div(){return t.element},get m(){return e._currentMolView()},set m(o){o!=null&&o._internalMol!==void 0&&t.canvas.setMol(o._internalMol);},get helm(){return n},get options(){return {width:e._width,height:e._height}},setData(o,r){if(r!==\"helm\")throw new Error(`LegacyAppWrapper: only 'helm' format supported (got '${r}').`);t.setHelm(o);},setHelm(o){t.setHelm(o);},setMol(o){t.canvas.setMol(o._internalMol);},getHelm(o){return t.getHelm()},getMolfile(){return e._service.getMolfile(t.getHelm())},resize(o,r){e._resize(o,r);},setSize(o,r){e._resize(o,r);},redraw(){t.canvas.redraw();},reset(){t.setHelm(\"\");},getFormula(o){return yl(fe(t.canvas.getMol()))},getMolWeight(){return De(t.canvas.getMol())},getExtinctionCoefficient(){return Oe(t.canvas.getMol())},getDrawOptions(){return e._drawOptions}}}_currentMolView(){let e=this._app.canvas.getMol(),t=se(e),n=this._app.canvas.getSelection();if(!n.isEmpty)for(let o of t.atoms){let r=o.bio.id;typeof r==\"number\"&&(o.selected=n.atoms.has(r));}return t}_resize(e,t){this._width=e,this._height=t,this._app.canvas.resize(e,t);}calculateSizes(){let e=zi(this._host.clientWidth,this._width),t=zi(this._host.clientHeight,this._height);this._resize(e,Math.max(50,t-this.toolbarheight));}destroy(){if(!this._destroyed){this._destroyed=true;for(let e of this._unsubs)e();this._unsubs.length=0,this._app.destroy();}}};function yl(i){let e=[];for(let[t,n]of i.elements.entries())e.push(n===1?t:`${t}${n}`);return e.join(\"\")}function zi(i,e){return typeof i!=\"number\"||isNaN(i)||i<=0?e:i}var gl=240,_l=80,_t=class{constructor(e,t,n){this._tooltip=null;this._destroyed=false;this.name=e,this._service=t;let o=n?.documentImpl??vl();if(o===null)throw new Error(\"LegacyInputWrapper: no Document available.\");this._doc=o,this._host=v(this._doc,\"div\",{class:\"hwe-legacy-input\",\"data-testid\":\"legacy-input-host\"}),this.viewer=new ae(this._host,t,{width:n?.editorOptions?.width??gl,height:n?.editorOptions?.height??_l,documentImpl:this._doc});}get value(){return this.viewer.editor.getHelm()}set value(e){this._ensureLive(),this.viewer.editor.setHelm(e);}get molValue(){return this.viewer.editor.m}set molValue(e){this._ensureLive(),this.viewer.editor.setMol(e);}redraw(){this._ensureLive(),this.viewer.editor.redraw();}showTooltip(e,t){this._ensureLive(),this._tooltip!==null&&this._tooltip.parentNode!==null&&this._tooltip.parentNode.removeChild(this._tooltip);let n=v(this._doc,\"div\",{class:\"hwe-legacy-input__tooltip\",\"data-testid\":\"legacy-input-tooltip\",style:`position: absolute; left: ${t.p.x}px; top: ${t.p.y}px;`});typeof e==\"string\"?n.appendChild(this._doc.createTextNode(e)):n.appendChild(e),this._host.appendChild(n),this._tooltip=n;}destroy(){this._destroyed||(this._destroyed=true,this._tooltip!==null&&this._tooltip.parentNode!==null&&this._tooltip.parentNode.removeChild(this._tooltip),this._host.parentNode!==null&&this._host.parentNode.removeChild(this._host));}getHost(){return this._host}getTooltip(){return this._tooltip}_ensureLive(){if(this._destroyed)throw new Error(\"LegacyInputWrapper: this instance has been destroyed.\");this._service;}};function vl(){return globalThis.document??null}var xl=/^R([1-9][0-9]*)$/,Wi=new Set([x.PEPTIDE,x.RNA,x.CHEM,x.BLOB]),wl=new Set([\"Backbone\",\"Branch\",\"Terminal\",\"Undefined\"]);function Ki(i){if(typeof i.symbol!=\"string\"||i.symbol.length===0||typeof i.molfile!=\"string\"||!Wi.has(i.polymerType)||!wl.has(i.monomerType))return null;let e=[];for(let n of i.rgroups??[]){if(typeof n.label!=\"string\"||!xl.test(n.label))continue;let o={label:n.label,capGroupName:typeof n.capGroupName==\"string\"?n.capGroupName:\"\",capGroupSMILES:et(n)??\"\"};typeof n.alternateId==\"string\"&&(o.alternateId=n.alternateId),e.push(o);}let t={symbol:i.symbol,molfile:i.molfile,polymerType:i.polymerType,monomerType:i.monomerType,rgroups:e};return typeof i.name==\"string\"&&(t.name=i.name),typeof i.smiles==\"string\"&&(t.smiles=i.smiles),typeof i.naturalAnalog==\"string\"&&(t.naturalAnalog=i.naturalAnalog),i.meta!==void 0&&i.meta!==null&&(t.meta={...i.meta}),typeof i.author==\"string\"&&(t.author=i.author),i.createDate!==void 0&&(t.createDate=i.createDate),typeof i.id==\"number\"&&(t.id=i.id),t}function kl(i){return i===x.PEPTIDE?g.AA:i===x.RNA?g.SUGAR:i===x.CHEM?g.CHEM:i===x.BLOB?g.BLOB:g.AA}function Xn(i,e,t){if(i===x.PEPTIDE)return g.AA;if(i===x.CHEM)return g.CHEM;if(i===x.BLOB)return g.BLOB;if(i===x.RNA){if(e===\"Branch\")return g.BASE;if(e===\"Backbone\")return t===\"P\"||t===\"p\"?g.LINKER:g.SUGAR}return g.AA}function Al(i,e){let t=i.subscribe(e);return ()=>{t!=null&&typeof t.unsubscribe==\"function\"&&t.unsubscribe();}}var en=class{constructor(e,t){this._cache=new Map;this._polymerTypesCache=null;this._version=0;this._base=e,this.source=t??(typeof e.source==\"string\"?e.source:\"datagrok-bridge\"),this.onChanged=new Z,this._unsub=Al(e.onChanged,()=>{this._cache.clear(),this._polymerTypesCache=null,this._version+=1,this.onChanged.next({type:\"reload\"});});}get version(){return this._version}get isEmpty(){return typeof this._base.isEmpty==\"boolean\"?this._base.isEmpty:this.getPolymerTypes().length===0}getMonomer(e,t){let n=`${e}|${t}`;if(this._cache.has(n))return this._cache.get(n)??null;let o=this._base.getMonomer(e,t),r=o==null?null:this._enrichColors(Ki(o));return this._cache.set(n,r),r}_enrichColors(e){if(e===null)return null;let t=this._base;if(typeof t.getMonomerColors!=\"function\")return e;let n=Xn(e.polymerType,e.monomerType,e.naturalAnalog),o=null;try{o=t.getMonomerColors(n,e.symbol);}catch{o=null;}if(o==null)return e;let r=o.backgroundcolor,s=o.textcolor,a=o.linecolor;if(typeof r!=\"string\"||typeof s!=\"string\"||typeof a!=\"string\")return e;let d={...e.meta??{},colors:{...e.meta?.colors??{},default:{line:a,text:s,background:r}}};return {...e,meta:d}}registerInlineSmilesMonomer(e,t){let n=this._base;typeof n.getWebEditorMonomer==\"function\"&&n.getWebEditorMonomer(kl(e),t);let o=n.getMonomer(e,t),r=o==null?null:this._enrichColors(Ki(o));if(r===null)throw new Error(`BridgedMonomerLib: could not register inline SMILES monomer '${t}'`);return this._cache.set(`${e}|${t}`,r),this._cache.set(`${e}|${r.symbol}`,r),r}getMonomerSet(e){let t=new Map;for(let n of this.getPolymerTypes())for(let o of this.getMonomerSymbolsByType(n)){let r=this.getMonomer(n,o);r!==null&&Xn(r.polymerType,r.monomerType,r.naturalAnalog)===e&&t.set(o,r);}return t}getMonomerSymbolsByType(e){return this._base.getMonomerSymbolsByType(e)}getByNaturalAnalog(e,t){let n=[];for(let o of this.getMonomerSymbolsByType(e)){let r=this.getMonomer(e,o);r!==null&&r.naturalAnalog===t&&n.push(r);}return n}getPolymerTypes(){if(this._polymerTypesCache!==null)return this._polymerTypesCache;let e=[],t=typeof this._base.getPolymerTypes==\"function\"?this._base.getPolymerTypes():Object.values(x);for(let n of t){if(!Wi.has(n))continue;let o=this._base.getMonomerSymbolsByType(n);Array.isArray(o)&&o.length>0&&e.push(n);}return this._polymerTypesCache=e,e}getColors(e,t){let n=t===\"dark\"?Ie:we,o=e===null?g.AA:Xn(e.polymerType,e.monomerType,e.naturalAnalog);return D(e,o,n)}addMonomer(e){throw new Error(\"BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.\")}removeMonomer(e,t){return  false}merge(e){throw new Error(\"BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.\")}toJSON(){let e=[];for(let t of this.getPolymerTypes())for(let n of this.getMonomerSymbolsByType(t)){let o=this.getMonomer(t,n);o!==null&&e.push(o);}return e}destroy(){this._unsub(),this.onChanged.complete(),this._cache.clear();}};function Jn(i,e){return new en(i,e)}var tn=class tn{constructor(e){this._overriddenFuncs=null;this._originalFuncs=null;this._molfilesEditor=null;this._molfilesEditorHost=null;this._molfilesGcTimer=null;if(e.service===void 0||e.service===null)throw new TypeError(\"HelmHelperAdapter: options.service is required\");this._service=e.service,this.seqHelper=e.seqHelper??null,this._logger=e.logger??new Ce,this._bridge=e.monomerLibBridge??(t=>Jn(t)),this._doc=e.documentImpl??ji();}get service(){return this._service}createHelmInput(e,t){let n={...t};return n.documentImpl===void 0&&this._doc!==null&&(n.documentImpl=this._doc),new _t(e,this._service,n)}createHelmWebEditor(e,t){let n=e??this._createDetachedHost();return new ae(n,this._service,{...t?.width!==void 0?{width:t.width}:{},...t?.height!==void 0?{height:t.height}:{},...this._doc!==null?{documentImpl:this._doc}:{}})}createWebEditorApp(e,t){return new gt(e,this._service,{...t!==void 0?{initialHelm:t}:{},...this._doc!==null?{documentImpl:this._doc}:{}})}get originalMonomersFuncs(){return this._originalFuncs}buildMonomersFuncsFromLib(e){let t=this._bridge(e),n=e;function o(s,a){if(typeof n.getWebEditorMonomer==\"function\"){let p=n.getWebEditorMonomer(s,a);if(p!=null)return p}let{biotype:d,symbol:l}=qi(s,a);if(l===null)return null;let u=Tl(l),c=Yi(d),m=t.getMonomer(c,u);return m===null?null:Xi(m,u)}function r(s){let{biotype:a}=qi(s,void 0),d=Yi(a),l={};for(let u of t.getMonomerSymbolsByType(d)){let c=t.getMonomer(d,u);c!==null&&(l[u]=Xi(c,u));}return l}return {getMonomer:o,getMonomerSet:r}}overrideMonomersFuncs(e){let t=this._overriddenFuncs;return this._originalFuncs===null&&(this._originalFuncs=t??this._defaultFuncs()),this._overriddenFuncs=e,t??this._originalFuncs}revertOriginalMonomersFuncs(){let e=this._originalFuncs??this._defaultFuncs(),t=this._overriddenFuncs??e;return this._overriddenFuncs=e,this._originalFuncs=null,t}getHoveredAtom(e,t,n,o){let s=new q(n._internalMol,$).test({x:e,y:t});if(s===null||s.atom===void 0)return null;for(let a of n.atoms)if(a.bio.id===s.atom.id||a.bio.id===void 0&&a.bio.continuousId===s.atom.bio.continuousId)return a;return null}getMolfiles(e){let t=this._ensureMolfilesEditor();t.editor.helm.noDraw=true;try{let n=[];for(let o of e){if(typeof o!=\"string\"||o.length===0){n.push(\"\");continue}t.editor.setHelm(o),n.push(t.editor.getMolfile());}return n}finally{t.editor.helm.noDraw=false,this._scheduleMolfilesEditorGc();}}parse(e,t){let n=this._service.parse(e,{mode:\"lenient\",resolveMonomers:false}),o=oe(n.mol);return se(o)}removeGaps(e){let t;try{t=this._service.removeGaps(e);}catch(o){throw o instanceof j&&o.type===void 0&&(o.type=\"HelmNotSupportedError\"),o}let n=Ml(this._service,e);return {srcHelm:t.srcHelm,resHelm:t.resHelm,monomerMap:n?new Map(t.monomerMap):null}}destroy(){this._molfilesGcTimer!==null&&(clearTimeout(this._molfilesGcTimer),this._molfilesGcTimer=null),this._removeMolfilesEditorNow();}_defaultFuncs(){return {getMonomer:(e,t)=>null,getMonomerSet:e=>({})}}_createDetachedHost(){let e=this._doc??ji();if(e===null)throw new Error(\"HelmHelperAdapter: no Document available\");let t=e.createElement(\"div\");return t.style.width=\"0px\",t.style.height=\"0px\",t.style.position=\"fixed\",t}_ensureMolfilesEditor(){if(this._molfilesEditor!==null)return this._molfilesGcTimer!==null&&(clearTimeout(this._molfilesGcTimer),this._molfilesGcTimer=null),this._molfilesEditor;let e=this._createDetachedHost();return this._molfilesEditorHost=e,this._molfilesEditor=new ae(e,this._service,{width:100,height:100,...this._doc!==null?{documentImpl:this._doc}:{}}),this._logger,this._molfilesEditor}_scheduleMolfilesEditorGc(){this._molfilesGcTimer!==null&&clearTimeout(this._molfilesGcTimer),typeof setTimeout==\"function\"&&(this._molfilesGcTimer=setTimeout(()=>{this._molfilesGcTimer=null,this._removeMolfilesEditorNow();},tn._MOLFILES_GC_MS));}_removeMolfilesEditorNow(){this._molfilesEditor=null,this._molfilesEditorHost!==null&&this._molfilesEditorHost.parentNode!==null&&this._molfilesEditorHost.parentNode.removeChild(this._molfilesEditorHost),this._molfilesEditorHost=null;}};tn._MOLFILES_GC_MS=1e3;var vt=tn;function ji(){return globalThis.document??null}function Ml(i,e){try{let t=i.parse(e,{mode:\"lenient\",resolveMonomers:!1});for(let n of t.mol.atoms)if(n.symbol===\"*\")return !0;return !1}catch{return  false}}function Tl(i){return i.length>=2&&i.charAt(0)===\"[\"&&i.charAt(i.length-1)===\"]\"?i.slice(1,i.length-1):i}function qi(i,e){if(typeof i==\"string\")return {biotype:i,symbol:e??null};if(i!==null&&typeof i==\"object\"&&i.T===\"ATOM\"){let t=i;return {biotype:t.bio.type,symbol:e??t.elem}}return {biotype:g.AA,symbol:e??null}}function Yi(i){switch(i){case g.AA:return x.PEPTIDE;case g.SUGAR:case g.BASE:case g.LINKER:case g.NUCLEOTIDE:return x.RNA;case g.CHEM:return x.CHEM;case g.BLOB:return x.BLOB;default:return x.PEPTIDE}}function Xi(i,e){let t={};for(let o of i.rgroups)t[o.label]=o.capGroupName;let n={id:e??i.symbol,m:i.molfile,rs:i.rgroups.length,type:i.polymerType,mt:i.monomerType,at:t};return i.name!==void 0&&(n.n=i.name),i.naturalAnalog!==void 0&&(n.na=i.naturalAnalog),i.smiles!==void 0&&(n.smiles=i.smiles),n}function Sl(i,e){if(e==null)throw new TypeError(\"registerWithDatagrok: options is required\");let t=new vt({service:e.service,...e.seqHelper!==void 0?{seqHelper:e.seqHelper}:{},...e.logger!==void 0?{logger:e.logger}:{},...e.documentImpl!==void 0?{documentImpl:e.documentImpl}:{}}),n=()=>{};if(typeof e.libProvider==\"function\"){let o=e.libProvider;Promise.resolve().then(()=>o()).then(r=>{if(r==null)return;let s=r.onChanged.subscribe(()=>{t.buildMonomersFuncsFromLib(r);});n=()=>{s!=null&&typeof s.unsubscribe==\"function\"&&s.unsubscribe();};}).catch(()=>{});}return {adapter:t,unsubscribe(){n();}}}\nexport{We as AtomPropsDialog,ft as AtomicStructurePane,je as BondPropsDialog,en as BridgedMonomerLib,Ke as ChooseRDialog,Gi as DEFAULT_TOOLBAR_BUTTONS,Fe as EventBus,bt as ExtraPane,qe as FindReplaceDialog,at as HelmEditor,yt as HelmEditorApp,vt as HelmHelperAdapter,j as HelmNotSupportedError,F as HelmParseError,Vn as HelmService,g as HelmTypes,Ze as HelmValidationError,Ge as HistoryStack,P as HwError,gt as LegacyAppWrapper,ae as LegacyEditorWrapper,_t as LegacyInputWrapper,hn as MonomerLib,rn as MonomerNotFoundError,ct as MonomerPalette,or as MonomerTypes,pt as NotationPane,x as PolymerTypes,ht as PropertiesPane,V as Selection,mt as SequencePane,ut as Toolbar,Ot as bondsOnAtom,Jn as bridgeMonomerLib,se as buildHelmMolView,In as darkTheme,Ss as defineTheme,Qt as extraPaneId,Zt as extraPaneSlug,W as freeRgroups,xa as hasFreeRgroup,$ as lightTheme,Sl as registerWithDatagrok,bi as takenRgroups,be as totalRgroups};","// HELM type vocabulary is owned by `@datagrok-libraries/hwe` (the standalone\n// HELM editor) and re-exported here as the single source of truth. The string\n// values match the canonical Pistoia HELM Web Editor, except `NUCLEOTIDE` which\n// uses the corrected spelling `HELM_NUCLEOTIDE` (was `HELM_NUCLETIDE`).\nimport { HelmTypes, MonomerTypes, PolymerTypes } from '@datagrok-libraries/hwe';\nexport { HelmTypes, MonomerTypes, PolymerTypes };\n// hwe migration: these two small enums are not part of the hwe value vocabulary.\n// They are defined here locally (replicating the legacy HELM Web Editor values)\n// so `@datagrok-libraries/bio` no longer depends on\n// `@datagrok-libraries/helm-web-editor`.\nexport var MonomerNumberingTypes;\n(function (MonomerNumberingTypes) {\n    MonomerNumberingTypes[MonomerNumberingTypes[\"default\"] = 0] = \"default\";\n    MonomerNumberingTypes[MonomerNumberingTypes[\"continuous\"] = 1] = \"continuous\";\n})(MonomerNumberingTypes || (MonomerNumberingTypes = {}));\nexport var HelmTabKeys;\n(function (HelmTabKeys) {\n    HelmTabKeys[\"Sequence\"] = \"sequence\";\n    HelmTabKeys[\"Helm\"] = \"notation\";\n    HelmTabKeys[\"Properties\"] = \"properties\";\n    HelmTabKeys[\"StructureView\"] = \"structureview\";\n})(HelmTabKeys || (HelmTabKeys = {}));\n//# sourceMappingURL=consts.js.map","import { PolymerTypes } from '../helm/consts';\nexport const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: PolymerTypes.RNA, symbol: 'd' },\n    RIBOSE: { polymerType: PolymerTypes.RNA, symbol: 'r' },\n    PHOSPHATE: { polymerType: PolymerTypes.RNA, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\n/** Role of an entry in a HELM RNA splitted sequence.\n * SUGAR/BASE/PHOSPHATE are the standard triple positions.\n * TERMINAL_5P marks a 5'-end terminal modifier (e.g. Chol) — a monomer\n * with R2 only that takes the place of the leading sugar.\n * TERMINAL_3P marks a 3'-end terminal modifier (e.g. GalNAc) — a monomer\n * with R1 only that takes the place of the trailing phosphate. The OH cap\n * MUST be omitted when a TERMINAL_3P is present. */\nexport var NucleotideRole;\n(function (NucleotideRole) {\n    NucleotideRole[NucleotideRole[\"SUGAR\"] = 0] = \"SUGAR\";\n    NucleotideRole[NucleotideRole[\"BASE\"] = 1] = \"BASE\";\n    NucleotideRole[NucleotideRole[\"PHOSPHATE\"] = 2] = \"PHOSPHATE\";\n    NucleotideRole[NucleotideRole[\"TERMINAL_5P\"] = 3] = \"TERMINAL_5P\";\n    NucleotideRole[NucleotideRole[\"TERMINAL_3P\"] = 4] = \"TERMINAL_3P\";\n})(NucleotideRole || (NucleotideRole = {}));\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { MonomerTypes, PolymerTypes } from '../helm/consts';\n// hwe exports the HELM type vocabulary as `as const` objects (value-only), not\n// TS enums, so we re-create the value+type duality the old `import X = Enum`\n// aliases provided — consumers use these both as a value (`.RNA`) and as a type.\nconst HELM_POLYMER_TYPE = PolymerTypes;\nconst HELM_MONOMER_TYPE = MonomerTypes;\nexport { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };\n// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\n/** Tag on Monomer columns storing the nqName of a function that returns an IMonomerCanonicalizer.\n *  The `.%` prefix ensures this tag is persisted with projects. */\nexport const MONOMER_CANONICALIZER_FUNC_TAG = '.%monomer-canonicalizer-func';\n/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\n        return 'Custom';\n    }\n    ;\n    /** flag to let bio know if this provider implements method for converting helm to it */\n    static get implementsFromHelm() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\n        // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n        // @ts-ignore\n        if (window?.DG) {\n            // @ts-ignore\n            const constFuncs = window.DG.Func.find({ meta: { role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE } });\n            return Promise.all(constFuncs.map((f) => f.apply({})));\n        }\n        return [];\n    }\n}\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","import { HelmTypes, PolymerTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = PolymerTypes.RNA;\n            break;\n        case HelmTypes.AA:\n            polymerType = PolymerTypes.PEPTIDE;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = PolymerTypes.CHEM;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = PolymerTypes.BLOB;\n            break;\n        default:\n            polymerType = PolymerTypes.PEPTIDE;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap, NucleotideRole } from './types';\nimport { HELM_CORE_FIELDS, HELM_POLYMER_TYPE, HELM_MONOMER_TYPE, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (\n        // RNA: all branch monomers (bases) and all backbone monomers (sugars +\n        // phosphates, including modified ones). Modifications are looked up by\n        // symbol at assembly time, so they MUST be present in the formatted lib.\n        polymerType === HELM_POLYMER_TYPE.RNA || (polymerType === HELM_POLYMER_TYPE.PEPTIDE &&\n            it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== HELM_MONOMER_TYPE.BRANCH)) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly\n *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).\n * @param {number[]} chainStarts - Optional 0-based start positions of disjoint HELM chains.\n *   When more than one chain is present each chain is assembled independently and the\n *   chains are stacked vertically into a single molfile (multi-strand HELM support).\n * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles, chainStarts) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // Multi-chain HELM (e.g. RNA1{...}|RNA2{...}): assemble each disjoint chain\n    // on its own, then stack them vertically into a single molfile. Each chain\n    // reuses the exact single-chain assembly below, so its geometry, capping and\n    // per-monomer atom/bond map are unchanged; combineMolfilesVertically shifts\n    // the coordinates and re-bases the atom/bond indices and monomer-map keys.\n    if (chainStarts && chainStarts.length > 1) {\n        const parts = new Array(chainStarts.length);\n        for (let c = 0; c < chainStarts.length; ++c) {\n            const s = chainStarts[c];\n            const e = c + 1 < chainStarts.length ? chainStarts[c + 1] : monomerSeq.length;\n            const subSeq = monomerSeq.slice(s, e);\n            const subRoles = roles ? roles.slice(s, e) : undefined;\n            parts[c] = monomerSeqToMolfile(subSeq, monomersDict, alphabet, polymerType, subRoles);\n        }\n        return combineMolfilesVertically(parts, chainStarts);\n    }\n    // Triples mode is on only when the caller flagged the row with roles\n    // (built and validated by `buildRolesForHelmRna` in to-atomic-level.ts).\n    // The roles array carries the per-position semantics — including\n    // TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't\n    // re-validate the length here.\n    const triplesMode = polymerType === HELM_POLYMER_TYPE.RNA && !!roles &&\n        roles.length === monomerSeq.length;\n    // define atom and bond counts, taking into account the bond type\n    const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === HELM_POLYMER_TYPE.PEPTIDE)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        // Default sugar/phosphate are only consulted in bases-only mode. In\n        // triples mode, every nucleotide carries its own.\n        if (!triplesMode) {\n            sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n            phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        }\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        // In triples mode, the \"logical\" sequence length is the nucleotide count.\n        seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    if (triplesMode) {\n        runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);\n    }\n    else {\n        for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n            const seqMonomer = monomerSeq[v.i];\n            if (seqMonomer.symbol === GAP_SYMBOL)\n                continue;\n            const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n            lastMonomerCappingAtom = monomer.terminalR2Atom;\n            const mAtomFirst = v.nodeShift;\n            const mBondFirst = v.bondShift;\n            addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n            //adding stereo atoms to array for further STEABS block generation\n            monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n            nAtoms += monomer.atoms.x.length;\n            const mAtomCount = v.nodeShift - mAtomFirst;\n            const mAtomList = new Array(mAtomCount);\n            for (let maI = 0; maI < mAtomCount; ++maI)\n                mAtomList[maI] = mAtomFirst + maI;\n            const mBondCount = v.bondShift - mBondFirst;\n            const mBondList = new Array(mBondCount);\n            for (let mbI = 0; mbI < mBondCount; ++mbI)\n                mBondList[mbI] = mBondFirst + mbI;\n            monomers.set(v.i, {\n                biotype: seqMonomer.biotype,\n                symbol: seqMonomer.symbol,\n                atoms: mAtomList, bonds: mBondList\n            });\n        }\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {ISeqMonomer[]} monomerSeq - the sequence of monomers\n * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers\n * @param {ALPHABET} alphabet - the alphabet of the monomers\n * @param {PolymerType} polymerType - the type of polymer\n * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples\n * @param {Array} roles - per-position role tags (only meaningful when triplesMode is true)\n * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    let lastPhosphateGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (let i = 0; i < monomerSeq.length; ++i) {\n        const seqMonomer = monomerSeq[i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n        // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track\n        // the LAST one — its atoms/bonds are dropped at the 3'-terminus.\n        if (triplesMode && i % 3 === 2)\n            lastPhosphateGraph = lastMonomerGraph;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === HELM_POLYMER_TYPE.PEPTIDE) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)\n        void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it\n        // Per-monomer-loop already summed sugars + bases + phosphates for every\n        // entry in monomerSeq (terminals included). Reservation: each backbone\n        // emit (sugar / phosphate / terminal) reserves +1 bond slot for the\n        // chain-extending bond, each branch (base) reserves +1 for its branch\n        // bond. Total reservations = monomerCount.\n        bondCount += monomerCount;\n        // OH cap atom rides on the 3'-end. Skip it when HELM specified a\n        // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.\n        const has3pTerm = !!roles && roles.length > 0 &&\n            roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n        if (has3pTerm) {\n            needsCapping = false;\n            // Mirror the peptide branch (which does both atomCount-- and bondCount--\n            // when it skips the terminal cap). `bondCount += monomerCount` above\n            // reserves one chain-extending slot per monomer; the LAST monomer's slot\n            // is normally filled by the terminal OH cap bond. With a 3'-terminal\n            // modifier there is no cap, so that last reserved slot stays empty —\n            // leaving the declared bond count one higher than the emitted bond\n            // lines. Drop it so the V3000 COUNTS line matches the bond block exactly\n            // (otherwise the pre-OCL molfile is malformed and only survives because\n            // the OCL chirality pass re-derives the counts).\n            bondCount -= 1;\n        }\n        else\n            atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n    }\n    else { // nucleotides — bases-only legacy path with default sugar/phosphate\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n// Role-driven RNA assembly. Walks the monomers in chain order and emits\n// each one according to its NucleotideRole (assigned by `buildRolesForHelmRna`\n// from the library, not from a fixed triple index):\n//   - BASE                                  → branch monomer, attached to the\n//                                             branch point of the sugar most\n//                                             recently emitted.\n//   - SUGAR / PHOSPHATE / TERMINAL_5P / 3P  → backbone monomer, chained to the\n//                                             previous backbone unit.\n//\n// Because the role comes from chemistry, this transparently handles every\n// backbone layout — standard [sugar, base, phosphate] triples, a 5'-leading\n// phosphate, several phosphates / linkers in a row, a linker dropped in the\n// middle of the chain, missing trailing phosphate, and 5'/3' terminal\n// modifiers — without any index arithmetic. The first backbone monomer\n// naturally has no incoming chain bond (v.backboneAttachNode starts at 0),\n// and the trailing OH cap is added by the caller via needsCapping (skipped\n// when a TERMINAL_3P ends the chain).\nfunction runTriplesAssembly(monomerSeq, roles, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {\n    void LC; // assembly is driven by per-monomer roles, not by LC.seqLength\n    for (let i = 0; i < monomerSeq.length; ++i) {\n        const sm = monomerSeq[i];\n        if (sm.symbol === GAP_SYMBOL)\n            continue;\n        const role = roles[i];\n        const mG = getMolGraph(monomersDict, { symbol: sm.symbol, polymerType: helmTypeToPolymerType(sm.biotype) });\n        const aFirst = v.nodeShift;\n        const bFirst = v.bondShift;\n        v.i = i; // keep loop counter monotone (unused by nucleotide geometry)\n        if (role === NucleotideRole.BASE)\n            // Branch: attaches to v.branchAttachNode, set when the preceding sugar\n            // was emitted. Does not advance the backbone, so the next backbone unit\n            // still chains from that sugar's 3' side.\n            addBranchMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n        else\n            // Backbone: sugar / phosphate / linker / terminal modifier. Chains from\n            // the previous backbone unit (none for the very first one) and, for a\n            // sugar, sets up the branch attach point for the next base.\n            addBackboneMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n        mG.stereoAtoms?.forEach((s) => steabsCollection.push(s + getAtoms()));\n        addAtoms(mG.atoms.x.length);\n        const aList = [];\n        for (let a = aFirst; a < v.nodeShift; ++a)\n            aList.push(a);\n        const bList = [];\n        for (let b = bFirst; b < v.bondShift; ++b)\n            bList.push(b);\n        monomers.set(i, { biotype: sm.biotype, symbol: sm.symbol, atoms: aList, bonds: bList });\n    }\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n// Vertical gap (in molfile coordinate units) inserted between stacked chains\n// of a multi-strand HELM. Roughly two bond lengths — enough to read the strands\n// as separate without pushing them far apart.\nconst CHAIN_VERTICAL_GAP = 3.0;\nconst STEABS_MARKER = 'M  V30 MDLV30/STEABS ATOMS=(';\n/** Split `body` into its first `n` space-separated tokens plus a trailing\n * remainder token (so the result has n+1 entries). The remainder keeps any\n * embedded spaces of the tail verbatim.\n * @param {string} body - the line body to split\n * @param {number} n - number of leading tokens to peel off\n * @return {string[]} - the n tokens followed by the remainder */\nfunction splitLeadingTokens(body, n) {\n    const out = [];\n    let s = body;\n    for (let i = 0; i < n; ++i) {\n        const sp = s.indexOf(' ');\n        if (sp === -1) {\n            out.push(s);\n            s = '';\n            continue;\n        }\n        out.push(s.substring(0, sp));\n        s = s.substring(sp + 1);\n    }\n    out.push(s);\n    return out;\n}\n/** Extract the data lines (`M  V30 ...`) between a BEGIN/END marker pair.\n * @param {string} molfile - the V3000 molfile\n * @param {string} beginMarker - the block BEGIN marker line\n * @param {string} endMarker - the block END marker line\n * @return {string[]} - the data lines of the block, newline stripped */\nfunction extractBlockDataLines(molfile, beginMarker, endMarker) {\n    const begin = molfile.indexOf(beginMarker);\n    if (begin === -1)\n        return [];\n    const start = molfile.indexOf('\\n', begin) + 1;\n    const end = molfile.indexOf(endMarker, start);\n    return molfile.substring(start, end === -1 ? molfile.length : end)\n        .split('\\n')\n        .filter((l) => l.startsWith(C.V3K_BEGIN_DATA_LINE))\n        .map((l) => l.substring(C.V3K_BEGIN_DATA_LINE.length));\n}\n/** Parse a molfile produced by monomerSeqToMolfile back into atoms / bonds /\n * stereo-atom indices. Robust because we control the exact serialization\n * format; only the fields we need to renumber (indices) and shift (y) are\n * parsed, everything past them is preserved verbatim as an opaque tail.\n * @param {string} molfile - the V3000 molfile\n * @return {ParsedMol} - parsed atoms, bonds and STEABS atom indices */\nfunction parseGeneratedMolfile(molfile) {\n    const atoms = [];\n    for (const body of extractBlockDataLines(molfile, C.V3K_BEGIN_ATOM_BLOCK, C.V3K_END_ATOM_BLOCK)) {\n        // body: \"<idx> <type> <x> <y> <z> <...kwargs>\"\n        const t = splitLeadingTokens(body, 4); // [idx, type, x, y, tail]\n        atoms.push({ type: t[1], xStr: t[2], y: parseFloat(t[3]), tail: t[4] });\n    }\n    const bonds = [];\n    for (const body of extractBlockDataLines(molfile, C.V3K_BEGIN_BOND_BLOCK, C.V3K_END_BOND_BLOCK)) {\n        // body: \"<idx> <btype> <a1> <a2> <...cfg/kwargs>\"\n        const t = splitLeadingTokens(body, 4); // [idx, btype, a1, a2, tail]\n        bonds.push({ btype: t[1], a1: parseInt(t[2]), a2: parseInt(t[3]), tail: t[4] });\n    }\n    const steabs = [];\n    let idx = molfile.indexOf(STEABS_MARKER);\n    while (idx !== -1) {\n        idx += STEABS_MARKER.length;\n        const closeIdx = molfile.indexOf(')', idx);\n        // first entry inside the parens is the atom count, not an atom index\n        steabs.push(...molfile.substring(idx, closeIdx).split(' ').slice(1)\n            .map((s) => parseInt(s)).filter((n) => !Number.isNaN(n)));\n        idx = molfile.indexOf(STEABS_MARKER, closeIdx);\n    }\n    return { atoms, bonds, steabs };\n}\n/** Combine several already-assembled single-chain molfiles into one molfile,\n * stacking them vertically: the first chain keeps its coordinates, every\n * subsequent chain is shifted straight down so its top-most atom sits just\n * below the running bottom of everything placed so far. Atom / bond indices\n * and per-monomer maps are re-based, STEABS collections merged, and the\n * monomer-map keys offset by each chain's start position so the combined map\n * still keys by original flat HELM position.\n * @param {MolfileWithMap[]} parts - per-chain assembled molfiles (chain order)\n * @param {number[]} chainStarts - flat start position of each chain\n * @return {MolfileWithMap} - single combined molfile + merged monomer map */\nexport function combineMolfilesVertically(parts, chainStarts) {\n    const combinedAtomLines = [];\n    const combinedBondLines = [];\n    const combinedSteabs = [];\n    const combinedMap = new MonomerMap();\n    let atomOffset = 0;\n    let bondOffset = 0;\n    let runningBottom = Number.POSITIVE_INFINITY; // lowest y placed so far\n    let anyPlaced = false;\n    for (let c = 0; c < parts.length; ++c) {\n        const part = parts[c];\n        if (!part || !part.molfile)\n            continue;\n        const pm = parseGeneratedMolfile(part.molfile);\n        if (pm.atoms.length === 0)\n            continue;\n        let minY = Number.POSITIVE_INFINITY;\n        let maxY = Number.NEGATIVE_INFINITY;\n        for (const a of pm.atoms) {\n            if (a.y < minY)\n                minY = a.y;\n            if (a.y > maxY)\n                maxY = a.y;\n        }\n        // First placed chain keeps its coordinates; later chains drop below the\n        // current bottom, leaving CHAIN_VERTICAL_GAP between the strands.\n        const yShift = anyPlaced ? keepPrecision(runningBottom - CHAIN_VERTICAL_GAP - maxY) : 0;\n        for (let ai = 0; ai < pm.atoms.length; ++ai) {\n            const a = pm.atoms[ai];\n            const newIdx = atomOffset + ai + 1;\n            const newY = keepPrecision(a.y + yShift);\n            combinedAtomLines.push(C.V3K_BEGIN_DATA_LINE + newIdx + ' ' + a.type + ' ' + a.xStr + ' ' + newY + ' ' + a.tail + '\\n');\n        }\n        for (let bi = 0; bi < pm.bonds.length; ++bi) {\n            const b = pm.bonds[bi];\n            const newIdx = bondOffset + bi + 1;\n            const tail = b.tail ? ' ' + b.tail : '';\n            combinedBondLines.push(C.V3K_BEGIN_DATA_LINE + newIdx + ' ' + b.btype + ' ' + (b.a1 + atomOffset) + ' ' + (b.a2 + atomOffset) + tail + '\\n');\n        }\n        for (const s of pm.steabs)\n            combinedSteabs.push(s + atomOffset);\n        const posOffset = chainStarts[c] ?? 0;\n        for (const [pos, val] of part.monomers) {\n            combinedMap.set(posOffset + pos, {\n                biotype: val.biotype,\n                symbol: val.symbol,\n                atoms: val.atoms.map((x) => x + atomOffset),\n                bonds: val.bonds.map((x) => x + bondOffset),\n            });\n        }\n        const newBottom = keepPrecision(minY + yShift);\n        runningBottom = anyPlaced ? Math.min(runningBottom, newBottom) : newBottom;\n        anyPlaced = true;\n        atomOffset += pm.atoms.length;\n        bondOffset += pm.bonds.length;\n    }\n    if (!anyPlaced)\n        return MolfileWithMap.createEmpty();\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += C.V3K_BEGIN_COUNTS_LINE + atomOffset + ' ' + bondOffset + C.V3K_COUNTS_LINE_ENDING;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += combinedAtomLines.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += combinedBondLines.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (combinedSteabs.length > 0)\n        result += getCollectionBlock(combinedSteabs);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    return { molfile: result, monomers: combinedMap };\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, rolesList, chainStartsList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            const roles = rolesList ? rolesList[rowI] : undefined;\n            const chainStarts = chainStartsList ? chainStartsList[rowI] : undefined;\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles, chainStarts);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfiles: resMolList, warnings: molfileWarningList 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